Alphonse Elric

Alphonse Elric (アルフォンス・エルリック) is the secondary protagonist of the Fullmetal Alchemist series. The younger brother of Edward Elric, the Fullmetal Alchemist, Al is also a victim of the failed Human Transmutation experiment that lost Ed his right arm and left leg. Having had his entire physical being taken away from him in the aftermath of the tragedy, Alphonse exists solely as a soul alchemically bound to a large suit of steel armor. Now, Al travels with his brother in search of the legendary Philosopher's Stone, an item with the power to restore their bodies to normal.

Appearance
In his gunmetal-colored steel armor body, Alphonse stands out as one of the tallest characters in the series, inching out such stalwart man-mountains as Captain Buccaneer and Major Armstrong while absolutely dwarfing his older brother, who only comes up to his elbow in the beginning of the series. As such, a running gag in the series is that he is frequently mistaken for being the famous "Fullmetal Alchemist" in place of his brother - the rightful bearer of the title. The helmet that comprises Al's face is adorned with a large, conical horn in the middle of the forehead, has a pair of parallel, horizontal vents beneath each half-moon eye hole and a fang motif just above the protruding chin. The top of the helmet also sports a ribbon of white hair that hangs down to the small of the suit's back. Later in the series, the hair is cut short during a skirmish with the Fort Briggs Mountain Patrol, much to Al's chagrin.

The trunk of the body also consists of a removable breastplate with a protruding, triangular shelf on the chest just below the throat guard, a high collar that extends out of the back and surrounds the rear and sides of the neck, and a large, circular leather patch on either side of the abdomen.

A breechcloth covers the groin and painted on the left shoulder is a red Flamel, signifying Alphonse's tutelage under the master alchemist, Izumi Curtis.

Al's armor body also appears to have a triple spike motif, as each shoulder is adorned with a trio of large conical spikes lined in a row and each elbow, knee and foot carries small, spiky protrusions as well. Al also appears to have a white band around his right leg which holds up a small weapons holster.

Inside the empty armor is a curtain of chain mail for the protection of its former wearer as well as a small alchemical rune drawn in Edward's blood, which binds Al's soul to the metal by way of the iron in both. Al's "Blood Seal" is unique - likely of Edward's own design - and denotes a small flame locked in place by multiple intersecting polygons.

Human Form
In the manga, Alphonse's appearance before the accident was rather similar to his brother's. He was taller than Edward even then, despite being a year younger, and wore his golden-blond hair short and neat with a parting on the left side. His eyes - gold colored, like Ed's - are rounder than his brother's and set in a broader face, causing Al to more closely resemble Trisha than Edward, who resembles Van Hohenheim.

In Chapter 53, it is revealed that Al's body still exists, living without its soul inside the Gate. With absolutely no direct nourishment or maintenance, it has become skeletally thin, with its finger and toenails growing past his digits and its hair, though still parted on the left, growing past the shoulders in back and growing down over the right side of the face, all the way to its collarbone in the front. By the end of the series, after regaining his body, he is healthy and well-nourished again and years later is shown to have grown much taller.

In the 2003 anime series, Al's human appearance differs somewhat. His hair is a few shades darker than Edward's, and his eyes are brown instead of gold. The events of Conqueror of Shamballa depict Al donning a similar hairstyle to that of his older brother, with his bangs worn long, but still parted on the left rather than in the center, and a ponytail hanging down in back. He also dons an outfit identical to Ed's, including a pair of white gloves marked with Transmutation Circles.

Personality
In many ways, Alphonse's calm and passive disposition exists as a foil to his older brother's more abrasive personality. Al is kindhearted, notably compassionate and patient almost to a fault, acting often out of protective selflessness for his loved ones, new friends and sometimes toward even his enemies (Scar is a particular example). Having had his psychological growth stunted at the age of ten due to loss of his physical body, Alphonse retains a childlike purity in the face of all his encountered horrors; however, despite his age, he has always displayed a significantly higher level of maturity than Edward. Though Al is as passionate as his brother, he has remarked that his anger takes longer to spark and jokes that he is always beaten to the punch by Edward's outbursts.

On the other hand, Al's heart does contain some darkness born from the tragedies of his life. Plagued with insecurities about his own uncertain existence inside a suit of armor, Al craves the human warmth of his former life in desperate silence, fears that he will never again know closeness and is sometimes overwhelmed by the suspicion that he himself is not human. It is also revealed that Alphonse carries the added burden of blaming himself for the failure of his mother's resurrection and the subsequent loss of his brother's limbs.

As Edward detests his diminutive stature, Alphonse dislikes being reminded of his large size and often becomes melancholy when it inhibits or calls undue attention to him, lamenting that it was not his choice to become so big. As such, he displays a great deal of pleasure when others treat him as a child instead of the hulking brutish adult persona that his appearance gives off.

Possibly as part of his desire for warmth and love, Alphonse displays a great affection for small cats and has developed a bad habit of picking up stray kittens that he finds over the course of his travels, hiding them inside his armor cavity from his disapproving brother.

On a more subtle level, Alphonse appears to have a great fondness for women as well. Particularly sensitive himself, Alphonse has a gift for complimentary and inspirational speech that surpasses even that of his brother's. While this does not negate the effect his armor body has on ordinary girls, it does allow him to leave an impression on the few women with whom he regularly associates such as May Chang, Riza Hawkeye, Lan Fan and Sheska. When his skills are necessary, Alphonse is often paired up with female comrades in situations where Edward is not present. In many of the omake, Arakawa makes Al's primary motivation finding a girlfriend.

Aside from the warmth of physical contact, what Alphonse misses most about having a human body seems to be delicious food. He keeps a journal of all the various foods he will eat upon returning to his body in order to keep his spirits up (a practice encouraged by Edward) and has stated that his fondest wish is to have some of Winry's apple pie.

Relationships
Edward Elric - Alphonse's relationship with his older brother is easily the strongest and most significant of his personal relationships. Though the Elric brothers have wildly different personalities and argue often about the best way to go about things, they are close enough that each would readily and willingly give his life for the other. Alphonse is particularly supportive of his brother and holds a great deal of faith in him despite the fact that Edward almost constantly requires Al to look after him and keep him from getting into trouble. Edward is, himself, very protective of Al, but Alphonse's care of his brother has been described by Winry as being almost parental. While Ed continues to search feverishly for a way to return his brother to normal, Al refuses to be the only one to benefit and insists that he only wants to his human body again if Edward regains his right arm and leg by the same means.

Winry Rockbell - Born to the kind family that lived next door to the Elrics, Winry grew up alongside Ed and Al and means as much to them both as would a sister; she and Al are more than childhood friends, they are a family. However, Alphonse had displayed some sort of romantic affections for Winry in his youth, as revealed by his mention of how he and Ed had fought over her hand in marriage, but were both turned down. Nonetheless, Al expresses jealousy in one of the omake pieces over Edward's nearly seeing her naked in Chapter 84. For the most part, Al appears to have put those feelings behind him and takes pleasure in teasing Winry for her apparent feelings for his brother.

Izumi Curtis - As a former student of this spartan-minded alchemy mentor, Alphonse's respect for Izumi's great wealth of knowledge coupled with his memories of her harsh physical and spiritual training during his youth contribute to the fact that she is one of the few people of whom the brave young man is outright afraid. That being said, the time she spent raising Edward and Alphonse to be skilled alchemists and wise young men in general has left an immensely profound print on their hearts, causing them to see her (in her gentler moments) as a sort of surrogate mother, just as she seems to look at them as surrogate sons. Their relationship hits a strain with the boys' shame at having directly disobeyed her teachings, but when they own up to their transgression, Alphonse and Izumi are able to come to an understanding, not merely as master and student or as surrogate mother and son, but as friends and colleagues.

May Chang - Alphonse's relationship with May for most of the series is a one-sided crush, with her doting and lavishing praises on him while he seems to see her as no more than a friend and ally. However, his chivalrous and protective nature ensures that he takes on the task of her protection during their battles together. Her sudden attraction to Al is initially based on his own description of his human body in contrast to the appearance of his older brother. Al's interest in her appears to be largely intellectual, at least at first, as he hopes to learn alkahestry from her. However, their adventures in the North seem to have been leading towards a closer relationship, as each recognized in the other an intellectual equal. At the end of the series, Alphonse ventures to Xing to study alkahestry under May's tutelage and returns with her to Amestris some time later. It is implied by their joint return as well as May's presence in the new Elric Family Photo that the two have perhaps become romantically involved.

Abilities
Having apprenticed under the master alchemist Izumi Curtis, Alphonse has been trained to condition his body through regular workouts and sparring as part of her philosophy, "to train the spirit, first train the body." As such, Al has become a particularly competent hand-to-hand fighter, able to hold his own against armed opponents and even skilled martial arts practitioners. In fact, Edward had stated that Alphonse is an even more skilled combatant than himself and notes that he has never beaten him in a fight, even since before Izumi's training. Additionally, his armor body has several combat advantages including - strengthened offense and defense, imperviability to bullets, inexhaustible stamina, invulnerability against extreme temperatures and an exemption from needing to breathe, eat or sleep. Unfortunately, these are all tempered by the fact that he cannot take any actions that might cause the Blood Seal inside his armor to be damaged so as to prevent his soul from becoming detached.

Like his brother, Alphonse also wields a genius-level intellect and prodigious proficiency in the studies of biology, chemistry and alchemy. While Edward is apparently the greater mind of the two, Alphonse does not trail far behind and has been able to match wits with his brother since the days they learned alchemy together as children. Alphonse, skilled with words, is capable of solving complex alchemical puzzles and mysteries and has displayed an encyclopedic knowledge of his craft, but seems to lack Edward's amazing sense of focus, instead developing the social skills in which his older brother is so sorely deficient.

In the 2003 anime series, Alphonse would have become a State Alchemist alongside his brother but for the fact that the inclusion of a physical evaluation forced him to drop out of the program lest his secret be revealed. Otherwise, it is revealed that he was able to finish the written portion of the certification exam, a feat that most candidates, including Edward, were unable to match.

Alchemy
Alphonse is a particularly competent alchemist who transmutes quickly, cleanly and with remarkable attention to detail in the style of his master, Izumi. In combat, he uses alchemy to augment his offensive and defensive capabilities, crafting weapons for melee strikes and altering his surroundings to gain the advantage in the same way as his brother - transmuting columns, battering rams and traps for his enemies, albeit without the gaudy touches that Edward usually gives his works. While in general his alchemy is more conventional than that of Edward (who often uses it in unusual forms to outsmart his opponents), he has displayed greater creativity when the situation called for it. For instance, when equipped with a Philosopher's Stone, he was able to use his alchemy in unexpected ways, like transmuting flash bangs, flexible swords and conical earth-prisons to surprise his opponents.

However, Alphonse's own alchemy is unique in several ways that make themselves apparent over the course of the two diverging story lines. From the beginning of the story, it becomes clear that - unlike most alchemists - Al does not require direct physical contact with the transmutation arrays he draws in order to manipulate matter; merely by standing over a circle and applying concentration (sometimes displayed as his crossing one hand flat over the other with both palms facing down), he can manipulate matter without touching it - a feat that has yet to be displayed by any other human alchemist without an alchemical amplifier. This may be due to the nature of his existence as a soul inside a suit of armor, he may be able to protrude the influence of his soul over larger distances, unlike ordinary humans whose souls are confined within their skin.

In the manga, Alphonse gains the additional ability to transmute without having to draw a transmutation circle at all. Having passed through the Gate as a result of the failed Human Transmutation, the ability had remained dormant inside his soul so long as his more tragic memories of the event stayed repressed. But after he regains his memories in Chapter 30, Alphonse discovers that the skill he had watched his brother and master perform so many times now belonged to him as well and puts it into practice for the first time in Chapter 33.

In the 2003 anime, Alphonse gains the ability to transmute without a circle in another manner - by becoming the Philosopher's Stone himself due to Scar's machinations. At first, this seems like a boon because the properties of his armor are changed and his blood seal becomes impervious to damage, but it becomes apparent that Alphonse, as the stone, reacts dangerously with any nearby transmutations and loses a physical part of his body whenever he is used directly as an alchemical amplifier. In Conqueror of Shamballa, Alphonse's alchemy takes yet another transformation. Now unable to transmute without circles, he wears a pair of white gloves with transmutation circles in order to use alchemy quickly - emulating his older brother. Additionally, due to the instability of his soul after having his body changed so many times (from human, to steel, to Philosopher's Stone and back to human), Alphonse has gained the ability to split his soul into pieces and insert them into inanimate objects to act as golems. While in this state, he is able to see from the perspective of and communicate through his various avatars.

History
Born the second son of Trisha Elric and Van Hohenheim of Resembool in the year 1900, Alphonse's first few years were relatively peaceful and happy despite the short-lived abuse of his older brother Edward; but after the sudden disappearance of his father during the toddler's formative years, Al was left with his mother and brother as his only family. The three Elrics lived in peace in the rural village and the boys began displaying a remarkable talent for alchemy at a young age, much to the joyful astonishment of their mother. However, early in the year 1904, Trisha contracted an illness that had been spreading in the area and died, leaving her two sons orphaned. Alphonse, devastated by the loss of his mother, began to fear that he and his brother would not be able to survive without her, but twisted hope returned to the boy's heart when Edward vowed that the two of them would find a way to bring their dear mother back to life with the power of alchemy.

Alphonse and Edward spent the next few years living on their own in the Elric family home, supported by their close childhood friend Winry Rockbell and her grandmother Pinako, while pursuing the alchemical knowledge necessary for their planned resurrection. Although they had gained a great deal of information and comprehension regarding the extended basics of the craft, before long it became apparent to the young prodigies that there was only so far they could go while being self-taught. In a stroke of good fortune, Resembool was visited by an exceptionally skilled alchemist named Izumi Curtis who, after some persuasion, agreed to take the Elric brothers on as her apprentices provided they pass a preliminary test. She brought the boys to Yock Island near the town of Dublith in the southern region, where she informed them that they were to survive for one full month without alchemy. If, at the end of their ordeal, they could correctly explain the concept "One is All and All is One", they would begin their training under her wing.

While there, the brothers discovered self-reliance and gained new abilities and insights relevant to living in the world under their own power from having to forage and hunt for food as well as fend off periodic attacks from Mason, an employee at the Curtises' butcher shop who had disguised himself as a masked wild man at Izumi's behest. Coming to understand together that, as humans, they are but a small part of the world and universe as a whole, but that the world and universe cannot exist without a collective of small parts, the boys were able to fully comprehend Izumi's riddle by the time she returned and, as such, the Elric brothers were subjected to Izumi's intensive alchemy and martial arts training for the next five months, growing significantly in both mind and body and gaining a great deal of alchemical knowledge before returning to Resembool. Though instructed specifically by Izumi to understand that death is an irreversible part of the flow of the world and that acceptance of such is important to the "One is All, All is One" concept, the boys dove headlong into their plan to resurrect their mother upon their homecoming, having advanced their knowledge while abroad and discovered the basics to a forbidden practice called Human Transmutation.

Devising a Human Transmutation Circle, amassing the elemental ingredients for an adult human body and offering their own blood as soul and biological data, the boys secretly initiated the Human Transmutation secretly in their home. Unfortunately, the Human Transmutation resulted in a Rebound; Alphonse and Edward were pulled into The Gate. Encountering the mysterious being called Truth, Alphonse was forced into the stream of the Gate's vast alchemical knowledge and forced to witness as the Truth stripped him of his physical body as toll for crossing into God's domain. Returned to the human dimension, Alphonse's errant soul attached itself to the soulless, inhuman creature that had resulted from the failed transmutation as it struggled futilely to survive. Incapable of sustaining life, the grotesque body died, allowing Alphonse's soul to once again wander toward the other side.

When Alphonse next regained consciousness, he discovered that his soul had been bound alchemically to an antique suit of armor with a Blood Rune, and that his brother was sitting in a pool of blood - his right arm and left leg "taken". With the trauma of the tragedy, Alphonse's memories of the Gate, the Truth and his existence in the failed body became repressed. In a panic, Alphonse carried his brother to the Rockbells' house, begging Pinako to save Edward's life. During the night, after Edward's emergency surgery was completed successfully, Alphonse discovered the true tragedy of his new body. Incapable of physical sensation and sleep, he began to feel detached from others and lamented the long solitude of restless night.

The two boys remained in a lamentable state of shame and grief over their tragedy for some time, until the visiting officer Roy Mustang confronted Edward and persuaded him to join the State Alchemist program. Promising to use the system to find a way to restore their bodies, Edward underwent an operation to attach custom-built automail and, a year later, he applied for a received his state certification. On October 3rd of 1911, the boys burnt down their family home and left Resembool on a journey to return to normal.

Adventures in the East
Three years later, at the start of the story, Edward and Alphonse visit the eastern frontier town of Reole following a lead on what they consider their best chance at restoration - the legendary Philosopher's Stone. They infiltrate the town's newfound Church of Leto with the help of a young Letoist girl named Rosé in order to investigate the mysterious priest Cornello who claims to use divine powers to bring about miracles. With Edward suspecting that Cornello is in possession of the Philosopher's Stone, Alphonse helps expose the priest as a fraud and reveal his plan to fool the people of Reole for his own militaristic goals. Unfortunately, as the faux clergyman is defeated, the stone Cornello holds shatters and disintegrates. Coming to the conclusion that his stone, too, was a fake, Ed and Al set off on their next assignment, but not before informing the distraught and now spiritually perplexed Rosé that she is able to move forward even without her faith so long as she has her two strong legs and the truth.

After liberating the town of Youswell from the clutches of the corrupt Lt. Yoki and thwarting a train hijacking, the boys arrive in East City, where Colonel Mustang introduces them to state-certified bio-alchemist Shou Tucker, whom they hope can use his expertise on chimeric alchemy to give them some insight on a different means of restoring their bodies. Unfortunately, they discover that Tucker's famous past success in creating a chimera capable of human speech was the result of a human experimentation in which he sacrificed the life of his "estranged" ex-wife and that his fresh triumph was willingly gained at the cost of his young daughter Nina, to whom the boys had grown quite close.

While Alphonse and Edward suffer the grief of Nina's tragedy, they learn that Tucker and his mutilated daughter have been murdered by a mysterious assailant - the State Alchemist-targeting serial killer known only as "Scar", who then comes after Edward. Baffled by Scar's curious ability to alchemically destroy anything he touches with his right hand, the boys are soundly defeated, with large hole stretching from the hip to the shoulder being torn in the right side of Alphonse's armor body (taking off both his right arm and leg) and Edward's automail arm being completely destroyed. Alphonse is forced to watch in helpless horror as his broken older brother loses the will to fight and has Scar promise to leave his younger brother alone in exchange for his own life. Fortunately, Al's cries of protest are heard by Mustang's forces, who arrive on the scene before Scar can enact his lethal brand of justice. With the help of Major Alex Louis Armstrong, the Strong Arm Alchemist, Scar is driven away with his strange ability revealed to be a form of alchemy and his identity revealed to be an Ishvalan survivor of the Ishval Civil War. With the danger passed, Al berates his brother over his willingness to die and stresses the importance of staying alive no matter what.

With Major Armstrong as an escort, the two head back toward Resembool for repairs at the Rockbell house, but get sidetracked when they encounter Dr. Marcoh, an Ishval War deserter who had been researching the creation of the Philosopher's Stone. After some coaxing, Marcoh reveals to them the secret location of his research notes - the National Central Library - and expresses his hope that the brothers will be able to find the "truth behind the truth" of the hellish pursuit. Arriving in their hometown, Edward has his arm rebuilt in three days an then goes to work repairing Al's armor in a manner that does not harm the blood rune inside. They then begin the trek for Central City and the Marcoh's hidden notes.

Central City and Laboratory #5
Upon arriving in Central, the Major relinquishes his position as the boys' bodyguard to resume his normal duties, but appoints two of his own subordinates - 2nd Lieutenant Maria Ross and Sergeant Denny Brosh - to remain as Fullmetal's escorts since Scar is still at large. With their new guards in tow, Edward and Alphonse head to the National Central Library to find Marcoh's hidden journals, but are dismayed to find that the library's first branch and all the texts within had been completely destroyed in a suspicious fire just one day before their arrival. They are referred to a woman named Sheska, who had previously worked in the first branch and has a remarkable knowledge of all the texts that were held therein. Though she confirms that Dr. Marcoh's notes had indeed been in the first branch - and, therefore, incinerated - Sheska is able to recreate the entirety of the journal word-for-word due to her photographic memory. Discovering that Marcoh had coded his sensitive research notes in the guise of a cookbook, Edward and Alphonse compensate Sheska for her help and get to work deciphering the code. After ten grueling days of poring over Marcoh's text as well as a score of alchemical reference materials in the Central Library, the boys finally decrypt the journals and come to the horrific truth alluded to by the doctor himself - that the legendary Philosopher's Stone is created from live human beings.

Having reached such a devastating conclusion, the brothers are thrown into a deep despair, in which Edward suddenly brings up the fact that he has a question for Alphonse that he has always been too afraid to ask. Before Alphonse can hear the query, however, the brothers are interrupted by Armstrong, Ross and Brosh, who have all become informed about the terrible developments. However, their attempts to comfort the Elrics remind Edward that Marcoh had mentioned cryptically that there had been a "truth behind the truth" and the investigation resumes with renewed vigor. Looking into the matter of the alchemical laboratories within the city limits, they discover that the supposedly unused Fifth Laboratory is located next to the city's prison and, using the idea of the Philosopher's Stone's makeup as a base, posits that death row inmates may have been smuggled into Lab 5 to be secretly used in the stone's creation. With such a politically charged suspicion making direct inquiry difficult, the brothers make plans to sneak off and investigate the facility under cover of night, without informing their bodyguards.

Arriving at the lab, they discover several points that make it clear that the "decommissioned" building is still in use and Edward opts to slip inside to get a closer look, while Al remains outside because of his size and conspicuousness. However, Al doesn't have to wait long before the Lab begins to show signs of activity; he is attacked by a mysterious armored figure calling himself Number 66 and claiming to be charged with eliminating anyone who intrudes on Laboratory 5 in pursuit of its secrets. When Alphonse realizes that his new opponent is a disembodied soul bound to an empty suit of armor, just like him, 66 reveals his origins as an infamous serial killer named "Barry the Chopper" who had been pulled off death row and bound to a suit of armor by Lab 5 scientists hoping to experiment with his body and soul. Taken aback by the similarities and high combat strength of his "prey", Barry begins to taunt Alphonse, suggesting that the boy whose soul he claims to be had never existed and that his memories are all fabrications by his brother, substantiated by the people who pretend to have known him. Without the proof of his human body and remembering that Edward had mentioned a topic of discussion that he was too afraid to bring up, young Alphonse falls for Barry's ploy and becomes consumed with doubts about his own existence. Fortunately, as Number 66 is about to take advantage of Al's confusion, 2nd Lt. Ross and Sgt. Brosh arrive on the scene and open fire on his attacker. Suddenly, an explosion erupts within Lab 5, shaking the building to rubble as Alphonse watches in horror and cries out for his brother. Though Ross prevents Alphonse from entering the collapsing structure, an injured and unconscious Ed is carried out of the debris by a mysterious stranger. Not wishing to arouse military suspicion, Lt. Ross takes the brothers to a civilian clinic run by one of her friends.

Edward wakes the next day and by the time Winry arrives at the clinic to repair his damaged automail, Alphonse's doubts have stewed into a maelstrom of fear and anger. He confronts Edward angrily regarding the legitimacy of his soul and memories, but does not receive a straight answer from his brother, who retreats to the hospital roof, too upset to speak. However, a response does come in the form of a furious Winry, who assaults Al for his insensitive remarks and reveals that the topic of discussion Edward had been too afraid to bring up was whether Alphonse blames and resents his brother for the loss of his human body. Horrified by his own faithlessness and harsh words, Alphonse goes after his brother and the two reconcile, vowing to become stronger both mentally and physically so that they may someday restore themselves.

With that out of the way, the Elrics discuss the revelations of the Lab 5 incident with Major Armstrong, close friend and ally Lieutenant Colonel Maes Hughes and the Führer, who warns them all that the trail of the Philosopher's Stone may be far too dangerous to pursue any further. Having reached the limit of their investigative license in Central City, Edward and Alphonse make plans to visit their teacher in the southern region in order to strengthen their bodies and minds as well as consult Izumi on the Philosopher's Stone, Human Transmutation and the possibility of restoring their bodies. Winry, desiring to see the famous automail community of Rush Valley on the way to Dublith, tags along.

Journey to the South
As per Winry's request, the Elrics make a stop in Rush Valley to do some sightseeing; there, they meet the pickpocket Paninya, whose weaponized automail legs drive Winry to seek out their creator, Dominic LeCoulte, dragging Ed and Al along for the trip. After helping Dominic's daughter-in-law deliver a baby in a storm, the trio leaves the LeCoulte home, with Winry deciding to stay in Rush Valley as an apprentice in an automail atelier while Ed and Al continue on to Dublith.

Arriving in Dublith, the Elrics greet their Izumi and her husband Sig for the first time in four years. As they reminisce and share travel stories, the boys inquire about the Philosopher's Stone; although Izumi declares that she knows very little about the legend, she informs Ed and Al that she had recently encountered an alchemist in Central who appeared to know a great deal on the subject - an alchemist by the name of Van Hohenheim. Alphonse becomes excited at the mention of his father's name and asks Izumi to give them more information on the man, but Edward (still filled with resentment toward his estranged father) refuses outright to consult him. After observing the boys for the day, Izumi correctly perceives that her pupils' bodies have been altered as a result of an encounter with the Gate due to Human Transmutation and demands that they explain themselves fully.

After revealing everything that had transpired since they left Izumi, she comforts them unexpectedly and praises their alchemical skill in being able to survive the ordeal even in spite of her severe disappointment in their disobedience of her repeated warnings to stay away from Human Transmutation. She reveals that she, too, had made the mistake in her youth and had several of her internal organs "taken" by the Truth, owing to her frequent hematemesis. However, in accordance with her own principles, she expels the Elric brothers as her students and demands that they leave her house. They do so, but as Sig walks the two to the train station (while explaining that Izumi's Human Transmutation was an attempt to revive her stillborn child fifteen years prior), he informs the Elrics that they are welcome to address Izumi as a colleague now that they have been expelled, rather than as a superior, and can return to the Curtis home any time they wish. They turn back and request staunchly that Izumi help them find a way to restore their bodies. Reluctantly complying, Izumi puts forth a new idea; she asks Alphonse what he had seen when encountering the Truth inside the Gate when his body was taken, suggesting that with the huge toll he had paid to cross into god's domain, he likely saw a great deal more than either Ed or herself, who had only given up parts of themselves. However, Al remarks that he has no memory of anything that transpired between his disappearance from the human realm and his awakening inside the suit of armor. Deducing that Al's memories must have become repressed from the traumatic shock of the experience, Izumi declares that retrieving those memories may be the necessary key to unlocking the next stage in the Elrics' journey.

Ed and Al remain at the Curtis house for a few days to do research and train up while Izumi consults a doctor friend of hers on any possible methods of reversing amnesia, but things do not remain peaceful. While coming home from Dublith's library, the brothers are confronted by a strange person who seems to know their secret about Human Transmutation and Alphonse's body - secrets they have guarded from the government and the public rather carefully. Unfortunately, the man disappears suddenly before they can interrogate him, but a short while later - after Edward departs for South City alone to hand in his State Alchemist assessment - Alphonse is lured into a trap and captured by the stranger and three of his comrades, who take him to their secret base in the basement of the Devil's Nest pub to meet their boss - a mysterious man named Greed marked with the Ouroboros symbol.

While there, Alphonse discovers that the three who had abducted him as well as many others in their gang are Human Chimeras - something he had considered an impossibility. Martel, the young snake-chimera woman who had captured him by getting inside his armor and stalling his movements, explains that she (like several others) had been a soldier wounded in battle before military scientists experimented on her body, turning her into the being she is now.

Greed asks that the captive Alphonse reveal to him the method by which his soul was transfixed to a suit of armor, explaining that his ultimate agenda for possessing such knowledge is the pursuit of immortality as a living soul with a body incapable of death. Alphonse grows quickly weary of Greed's avaricious tirade and attempts to immobilize the man with some quick alchemy. It becomes clear, however, that Greed - like his human chimera flunkies - is also an alchemical impossibility. He demonstrates that he is a Homunculus, an artificially created human being with the power to regenerate immediately from any level of sustained physical damage, even those which would prove instantly fatal to normal humans.

Neither having been the one to perform the soul binding nor having any memories of the incident, Al attempts to explain that he cannot help Greed or his men, but as they protest, Izumi storms into their stronghold and trounces everyone standing in her way, having tracked Alphonse to this location. When it becomes clear that Izumi is no match for Greed's powers, Alphonse asks her to relay his location to Edward so that the brothers may decide what to do together, but after Ed arrives and refuses outright to cooperate with Greed's plans, the Homunculus orders his henchmen Roa, Martel and Dolcetto to flee with the armor boy in tow so that they may analyze him at their discretion. They escape through the sewers carrying Al, but are forced to leave him for safekeeping when it becomes apparent that soldiers have begun a raid on the bar; Roa and Dolcetto go off to fight while Martel is tasked with keeping Alphonse still from within.

Despite the hindrance, Al manages to overpower Martel enough to crawl slowly away until Greed - having escaped his fight against Edward - appears on the scene himself, followed immediately by Führer King Bradley. Al watches in amazement as the Führer engages Greed in combat, easily overwhelming the Homunculus by severing whole limbs with his sword faster than Greed can regenerate or even defend himself. Well aware that Martel would be thoroughly outclassed by the swashbuckling statesman, Alphonse vehemently refuses to let her exit the armor and help her battered boss. Roa and Dolcetto return to Al's side and request that he get Martel to safety as they free him from his chains and move to attack Bradley with fatal futility, but as Alphonse attempts to flee, Martel makes a move from within to attack the victorious Führer, who responds by plunging one of his swords deep into Al's armor body, killing her. As the slain woman's blood splashes on Al's blood rune and the trauma of what has just occurred in his body sets in, the memories of his sojourn into the Gate resurface and Alphonse loses consciousness. When he awakes, he is met by Ed, Major Armstrong and a cadre of Southern HQ soldiers who have opened up his chest cavity and pulled out Martel's lifeless body. Alphonse laments that he was unable to save Martel and, after Bradley interrogates Edward briefly on the national security implications of the incident, leaves freely with his brother for the Curtis house where the two discuss the occurrence at Devil's Nest more privately. Alphonse reveals to Edward that the ordeal and its various shocks have returned his memories of being inside the Gate, but that the information he regained did not include anything new on Human Transmutation. Edward, however, is more concerned with the Führer's actions in having every one of Greed's gang members slaughtered on the spot at Devil's Nest instead of leaving a few to be interrogated about Greed's obvious connection to the strange, Ouroboros-marked pair behind the manufacture of Philosopher's Stones in Central, despite having expressed a desire to get to the bottom of the matter. Suspicious of the military's motives, Edward suggests that they keep a close eye on Bradley's actions from here on.

Stranger from Xing and the Return to Central
With Ed's automail arm having sustained heavy damage in the fight against Greed, the Elrics depart from Dublith to visit Winry in Rush Valley for repairs. As Winry bludgeons Edward for wrecking her automail yet again, Alphonse reflects on the events in the southern region and begins to speculate whether the return of his memories grants him the same ability that it gave to his teacher and older brother - the ability to perform transmutations without the aid of a Transmutation Circle. While Winry prepares the necessary parts and materials, the Ed and Al wander around town, where Al's curious nature and love for strays leads him to a strange young man passed out from hunger in the street. Though Edward demands that his younger brother put the strange boy back where he found him, Al insists they treat the young man to a meal. The stranger introduces himself as Ling Yao, a traveler from the eastern nation of Xing and explains that he had crossed the Great Eastern Desert so as to see the ruins of Xerxes - the birthplace of alchemy - with his own eyes. When he reveals that he intends to research Amestrian alchemy and its differences from alkahestry, a native Xingese variation used primarily in medicinal practices, Edward and Al become excited at the prospects and ask Ling to demonstrate it for them, but Ling reveals that he is not an alkahestry practitioner. When asked why a non-practitioner would come all this way to study an art he cannot perform, Ling tells them that the only aspect of alchemy that interests him is a legend he had once heard - the legend of the Philosopher's Stone and its capacity to grant immortality.

The boys feign ignorance of the Stone and attempt to leave, but Ling sees through their ploy, immediately summoning his two armed bodyguards to detain them. Though Alphonse attempts to make peace through discussion, Edward predictably resists, prompting both of Ling's bodyguards to attack with Xingese martial arts; the ensuing fight spreads throughout the town with Alphonse combating the sword-wielding bodyguard Fu and Edward battling the kunai knife wielding Lan Fan. Alphonse encounters some difficulty trying to keep up with the remarkably quick-footed Fu, but when Paninya arrives to help, the young Elric concocts an idea. Asking Paninya to open fire on Fu with the grenade launching carbine in her left leg, Alphonse hides in the smoke and dust from the explosion so as to approach Fu unseen. Ambitious to test out his new abilities, Alphonse claps his hands together and transmutes, fastening Fu to a nearby billboard. Satisfied with his first successful, albeit sloppy, attempt at circle-less transmutation, Al takes his new captive and heads over to where Ed has defeated Lan Fan. As he arrives, Ling also appears on the scene and cleverly creates enough of a diversion for his two vassals to escape before fleeing himself. The Elrics return to Winry's place of business to find Ling already there and, after all the necessary repairs have been made to Edward's arm, reluctantly agree to let the young man and his cohorts tag along as they travel back to Central City.

Arriving at their destination, Ling's habit of wandering off kicks in and the party manages to lose him. Ignoring his absence, Ed and Al head with Winry to headquarters so as to greet Hughes and ask whether he had uncovered anything new pertaining to the investigation of those Ouroboros-bearers that they now suspect to be Homunculi like Greed. They are shocked to encounter Lt. Hawkeye and Colonel Mustang at headquarters, who state that they had both recently been transferred to the capital, but when the boys ask how Hughes is doing, Roy informs them that Maes has retired from the military and left for the countryside with his family. Disappointed, the Elrics find lodging at a local military-run hotel and attempt to continue the investigation on their own, but soon discover a horrible bit of news in the evening paper: that their friend Maria Ross has been convicted of Hughes' murder, which had apparently taken place a month prior. They rush off to confirm the information and coincidentally run into Ross herself, who is apparently fleeing from jail in the curious company of both Ling and Barry the Chopper, the soul bound armor guard that Alphonse had fought during the mission at Laboratory 5. While Barry keeps the Elrics occupied, Ross escapes on her own, but when the group observes a huge explosion over in the direction Maria was headed, Ed slips by and hurries to see what happened. Barry quickly flees the scene with Ling in tow, but Alphonse hangs back to demand of the Xingese traveler why he has partnered up with the Chopper. When Ling doesn't offer an answer, Alphonse rushes off to catch his brother and finds Edward suddenly attacking Colonel Mustang. Al holds Ed back, but when he asks what has happened, Edward reveals that the mysterious body on the ground at their feet, is that of Maria Ross, charred beyond all recognition by the Flame Alchemist's alchemy.

Roy offers no apology for killing Ross, but apologizes instead for keeping Hughes' death from them. The Elrics accompany the cleanup crew, including Major Armstrong, to the hospital where Dr. Knox reveals that the body he had just autopsied was so thoroughly burnt that only the dental records could be used to verify the corpse's identity. He admonishes Mustang, but to Edward's fury, the Flame Alchemist offers no further signs of remorse instead recommending that Armstrong - who is visibly distraught over his subordinate's violent death - take some time off in the east, where Roy claims the women are particularly beautiful. In the morning, the boys return to the hotel but find that Winry has disappeared; they deduce that Winry, having seen the report of Hughes' death, went off into town and their suspicions are confirmed when Gracia Hughes, Maes' widow, calls and asks them to come to her house and pick up their friend.

Arriving at the Hughes house, Ed and Al decide to set the record straight and explain the situation regarding Maes' death to Gracia, apologizing profusely for having drawn her late husband into such a dangerous situation. Having come to a solemn decision regarding the safety of those dear to him, Alphonse declares that, if it will cost other people their lives, he no longer wants his human body back. But both brothers are surprised when Gracia urges them to press on in the pursuit of their goal, telling them that her husband would want them to continue and their failure to do so would be to render Maes' death meaningless.

The Perilous Underground
The next morning, as the Elrics and Winry continue moping about their hotel, they receive a sudden visit from Major Armstrong, who says nothing but throws a heavy blow at Edward, denting his automail arm. Ignoring Ed and Al's protests, Armstrong declares that he will be taking Fullmetal to Resembool for repairs while Alphonse - who is too conspicuous - remains in the capital. Al and Winry remain utterly confused by this strange turn of events until Ling suddenly appears outside their hotel room window and explains the situation as he heard it from Barry the Chopper. Ling tells Al that Mustang had faked Maria Ross' death and arranged for her to sneak out of the country with the help of the Xingese travelers as part of an attempt to lure out the mysterious enemy that has been dogging them all this time; meanwhile, Edward's departure with Major Armstrong is part of a rendezvous mission wherein all involved parties pitting themselves against the elusive "Ouroboros gang" would sneak across the border to the ancient eastern nation of Xerxes in order to exchange and synchronize their collected information regarding their opponent. When a signal flare from Lan Fan ignites above the city, Ling announces that the second phase of the mission to "fish out" the enemy has begun. Alphonse declares that he will go with Ling in order to find out as much as possible and perhaps discover the identity of Hughes' killer. After Winry makes him promise to com home safely and tell her everything, the two set off in the direction of the flare.

When they arrive, however, they are shocked to find Lan Fan using her kunai throwing knives to attack a dog and are even more surprised when said dog metamorphoses into a human right before their eyes. While Ling comments that the strange young man that the dog has become gives off a strange aura, Al notices the Ouroboros tattoo on the mystery shape shifter's left thigh and recognizes him as the figure at Laboratory 5 whom Edward had stated was called "Envy". As Ling and Lan Fan engage Envy and Gluttony (another of his Ouroboros-marked comrades), Alphonse heads off to find the Colonel's group, encountering them as they prepare to chase after Barry - who is, in turn, pursuing a being explained to be his own human body with a lab animal's soul inside. Alphonse goes along with Roy, Hawkeye and 2nd Lt. Havoc explaining that the strange people with whom they have been dealing are Homunculi. Roy is skeptical even after Alphonse reveals the details of his encounter with Greed, but Lt. Hawkeye confirms Al's claim, stating that she had shot Gluttony several times in his vital areas, but was unable to bring him down.

Taking advantage of Barry's ability to sense his body's presence through his spirit, the party tails the errant creature to Central Alchemical Laboratory #3. At first, due to the lab's close connections to Central Command, the Colonel opts to end the mission here and regroup, but when Barry - crazed by the idea of being able to chop up his own body - rushes inside against orders, the foursome pursuing him storms in afterward, announcing to the staff inside that they are chasing a dangerous fugitive and misinforming them that backup is already on its way. The group follows the Barrys' trail to a sealed off basement level of the facility and decides to split up in order to find their quarry, Alphonse with Lt. Hawkeye and Colonel Mustang with 2nd Lt. Havoc.

Following Barry's trail, Al and Hawkeye arrive in a large, white room with huge stone doors at one end to discover that the Chopper has accosted and mutilated his human body, explaining that its advanced decomposition is due to the fact that the body and its new soul are incompatible and have been rejecting each other. Hearing this, Alphonse realizes that this is true for all incompatible alchemical unions and wonders just how long it will be before his own soul inevitably rejects his armor body.

Soon afterward, however, the three are joined by the Homunculus Lust, who laments Al's involvement in this excursion as it means she will have to set her mission back quite a bit by killing two Human Sacrifices in one night. Barry charges the Homunculus recklessly, but is swiftly cut to ribbons when Lust's fingernails extend into razor-sharp blades. Clearly intent to kill, Lust advances on Al and Hawkeye, asking aloud whether she should kill the armor boy first or send the lieutenant on ahead to join her commanding officer. Understanding that Lust's comments suggest that Roy has already been slain, Riza flies into a rage and unloads all of her firearms into the Homunculus' inhuman body to no effect before collapsing in anguish and despair. As Lust prepares to put the lieutenant out of her misery, however, Alphonse steps into her path to act as Riza's shield. He transmutes a lance and prepares to fight - prompting Lust to comment on his opening of the Gate and further bemoan the waste of such a promising Sacrifice - and demands that Lt. Hawkeye escape to safety, but as Lust effortlessly disarms him and begins carving away at his armor body, Riza remains in her dejected state and orders Alphonse to leave and save himself. Continuing to protect Lt. Hawkeye from Lust's vicious blows, Al refuses to leave and remarks that he rejects the idea of letting someone close to him die while he has the chance to save them. As he says this, Al hears Colonel Mustang's voice praise his valor and notices that Roy himself has entered the hall behind Lust. Realizing that the Flame Alchemist is about to begin an all-out onslaught on the Homunculus, Al quickly transmutes an earthen blast shield to protect Lt. Hawkeye and himself as Mustang unleashes wave after wave of conflagration on the inhuman Lust, not stopping until her Philosopher's Stone runs dry and her body crumbles to dust. With Lust dead, Riza and Al rush to the gravely injured Colonel's side, where Roy thanks Alphonse profusely for protecting the lieutenant.

After seeing Mustang and Havoc safely to the hospital, Alphonse heads back to the hotel to meet with Winry as promised. Though he looks much the worse for wear with parts of his armor missing and his right arm falling off, Winry welcomes him warmly.

Hunting Immortals
The following day, Alphonse heads to the hospital to visit the Colonel (while bringing Lan Fan along to detect the presence of any Homunculi who might wish to attack him) as well as discuss the previous night's mission. In addition to using Lt. Hawkeye's calculations to determine that the location of that large white hall could likely be somewhere beneath Central Command HQ and the Führer's executive residence, Alphonse relays information regarding the Führer's annihilation of the Devil's Nest gang before leaving.

As Edward has not yet returned from his excursion with Major Armstrong, Alphonse phones Pinako to find out whether or not he has arrived in Resembool yet. However, Pinako remarks that while Ed hasn't shown up in town, someone else has - the boys' father, Van Hohenheim. Returning to their room, Al explains the situation to Ling all while expressing his hope that Edward hasn't picked a fight with Hohenheim instead of trying to gain information. When Al explains that he himself doesn't hate his father - not remembering him particularly well from childhood - Ling discloses that his own paternal relationship is an odd one, as he is the 12th son of Xing's emperor. Elaborating that his search for the secret to immortality is for the purpose of gaining his ailing father's favor and rise to emperorship amid dozens of other siblings, Ling claims that Alphonse's current existence is the closest thing to real immortality. However, Alphonse himself explains that his metal body is not as convenient as one might think; as a human soul bound to a metal body, the instability of his existence means that, at any given time - in a year, a century or even a day - the two unlike essences may reject each other and Al will die just as suddenly or unexpectedly as anyone else. Horrified by this news, Winry reaffirms the necessity of returning Al to his human body as soon as possible, but Ling sees the situation differently. He argues that Al's soul could simply be transferred to another body before instability sets in and remarks that, not needing to sleep, eat or feel pain, Al's state is pretty ideal. This statement irritates Al, but before he can object, Winry explodes with fury, admonishing Ling for his insensitivity and ignorance before storming off to her room. Al follows to console her and jokes that she and Edward always get angry on his behalf before he gets the chance. Winry, contemplating all the suffering that Alphonse has endured, urges him to regain his human body as soon as possible.

When Ed returns to the hotel, he repairs Al's armor alchemically - albeit thinning out the metal in order to replace some of the missing pieces - and the brothers discuss their adventures apart. After Al explains the situation with the operation to flush out the Homunculi and the battle underground, Edward reveals some shocking information of his own. After encountering Van Hohenheim in Resembool, Ed had exhumed the remains of the creature that the boys had transmuted four years ago and discovered that it hadn't been their mother at all. But, as a result, he now believes that - rather than needing to fashion a new human body for Al's soul to inhabit - the armor boy can be returned to his original body. After Ed posits that Al's current existence would require the existence of his original, living body inside the Gate, Alphonse recalls - by way of the memories he had recovered in Dublith - his sojurn inside the Gate as well as his short time within the transmuted body. If Al's body is there inside the Gate, then all the Elrics have to do is go in and pull it out again just like Ed had done with Alphonse's soul. Just then, Ed is informed by the hotel desk clerk that he has received a call from Izumi, who confirms that the baby she had transmuted did not carry any traits similar to either her family or Sig's. She thanks Edward and hangs up again. When he tells this to Alphonse, the younger Elric explains that he feels the same gratitude, as he had blamed himself for years for forcing their mother to suffer through death a second time. Ed apologizes for putting his brother through that pain and sticking him with such an existence, but Al responds that he is just as culpable. Remembering all the suffering that has occurred as a result of their mistakes, Alphonse remarks that he had begun to believe that getting his body back wasn't worth further pain, but despite having come to understand that his current state doesn't make for an unbearable existence, he realizes that he no longer wants to spend his long nights awake and alone. With new resolve, the Elrics renew their promise to restore their bodies no matter what.

The boys consider their options, positing that the circumstances of their joint rebound may have caused their spirits to cross and intermix, allowing Alphonse's body to survive, but when the topic of using the Philosopher's Stone arises, the boys express their aversion to using human lives for personal gain and think of the Homunculi. Requiring more information, the Elrics decide that they will need a way to speak with a Homunculus directly. They head off to examine Laboratory 3 for a trace of the underground level, but find nothing, as the entrance has been alchemically effaced. As they wonder what their next move should be, the Elrics are met by Sgt. Brosh, who informs them that Scar has been sighted within the city and has apparently resumed his extermination of State Alchemists. Denny explains that their information regarding the killer has been updated with the fact that a large and ornate tattoo covers the entirety of Scar's right arm, jarring edward somewhat. Returning to their hotel room, edward explains to Alphonse that he hadmet a group of Ishvalans in the Eastern Desert who had known the Doctors Rockbell and had seen them die at the hand of a heavily bandaged warrior monk with a facial injury and a tattooed right arm - he believes that Scar is the man who murdered Winry's parents. With this in mind, Edward declares that they will need to confront Scar, not only to ask him about the Rockbells but also to lure out the Homunculi for questioning. Remembering that they were called "Human Sacrifices", Edward posits that whatever the Homunculi are planning requires the Elrics' participation, making their lives indispensable; if they appear to put themselves in mortal danger in a fight against Scar, the Homunculi will surely appear on the scene. Alphonse spots flaws in the plan, but when Ling and Lan Fan appear at the window, having overheard their conversation and offering their help in exchange for a part of the spoils when they manage to capture an immortal Homunculus, a joint plan comes together.

Over the next few days, Edward draws as much attention to himself as possible by going around town performing flashy alchemy for the citizens of the capital in an attempt to lure Scar out of the shadows. Presuming that Scar's presence around one of their precious Human Sacrifices will cause the Homunculi to take action, the Elrics have arranged for Ling and Lan Fan to lurk nearby on lookout for the monsters' unique presence. Taking notice of Fullmetal's odd behavior, Colonel Mustang and Lt. Hawkeye stop by to speak with them, but as the alchemists exchange information, Scar himself appears on the scene and attacks. Explaining their plan, the boys persuade Hawkeye and Mustang not to attack and enlist them in the plan by asking them to keep the Military Police from interfering. Flame and his adjutant escape while the Elrics engage the Ishvalan murderer.

The Northern Wall of Briggs
Ed and Al go to the north of the country to make a request to its guardian, Major General Olivier Mira Armstrong (Major Armstrong's sister) to help them look for the "Alkahestry girl," May Chang. Solf J. Kimblee arrives to keep an eye on them, bringing Winry as a hostage to prevent the Elrics from revealing Bradley's secret to Armstrong. However, during a confrontation with Scar and Kimblee's two chimeras the brothers manage to reach an agreement with them, Major Miles, May Chang and Winry. Alphonse convinces the chimeras, Zampano and Jerso that they may yet be able to get their old bodies back if they help the Elrics, and Winry reaches an uneasy truce with Scar. They agree to a plan whereby Scar will pretend to capture Winry, thereby allowing the two of them, with May, Marcoh, Zampano, Jerso, and Yoki to escape through a mine shaft back to Briggs, while Edward and Alphonse pretend to be furious that Scar has captured Winry.

However, the brothers quickly learn that Briggs has all but come under Kimblee's control, now that Major General Armstrong has killed General Raven and gone to Central to infiltrate high command. A blizzard sets in, which would prevent Edward from warning Winry's group, but since Alphonse's metal body is immune to cold he offers to go warn the group. On the way, however, Al blacks out (a disturbing occurrence as his metal body cannot sleep) and imagines himself before the Door, face-to-face with his emaciated human body. He becomes trapped in snow drifts, and May and Winry dig him out when they emerge from the mine shaft. Alphonse warns them not to return to Briggs, but blacks out again soon after--at the same time Edward nearly dies in the mine explosion in Baschool, suggesting that the Elrics' bodies and souls are connected as Edward had earlier theorized--so the group dismantles Alphonse's large body so he'll be easier to carry, and Scar leads them to a nearby Ishvalan village.

There, Alphonse awakens before he is put back together properly, while the group is poring over Scar's brother's research notebook. The idea of putting Al's pieces together gives May the idea to tear the binding off the notebook, thereby discovering the Nationwide Transmutation Circle. Then Alphonse's idea to flip the sheets of paper over leads to their discovery of Scar's brother's Reverse Transmutation Circle. As the group waits in the village, pondering this new knowledge, May attempts to teach Alkahestry to Al, but they become frustrated with each other, as May commands him repeatedly to "sense the veins of the Dragon" and Alphonse insists that he can't, and asks her to teach him the theory, to which May only responds "Look, I sense it!" When Envy shows up at the village, May uses long-distance alkahestry to frustrate him, then Marcoh reduces Envy to his true, worm-like form. Envy informs Al that Edward is missing after a mineshaft in Baschool collapses, but instead of rushing to look for him Al decides to remain with the group and press on with investigating the Nationwide Transmutation Circle, since that's what Al believes Edward would have done.

Scar gives Envy to May, telling her to return to Xing now that she has a clue to immortality that will save her clan, so she and Alphonse bid each other a tearful (in May's case) farewell, and Al promises to visit her in Xing to learn Alkahestry. Then Scar and Marcoh leave together and the rest of the group (Alphonse, Winry, Yoki, Zampano and Jerso) go to Reole, since by Al's calculations the tunnel for the circle would pass beneath it. There Al is reunited with his father, Hohenheim, for the first time in years. After the cold greeting he got from Edward only a few weeks before, Hohenheim expects similar treatment from Alphonse, but Al has no hesitation in calling Hohenheim 'Dad.' Hohenheim warns Al not to be so trusting, suggesting he might be working with Father, but then smiles, touched by his son's affection. He tells Alphonse his life story, including the creation of the Little One in the Flask. When Hohenheim expresses surprise that Alphonse so readily believed such a "crazy story," Alphonse suggests that the fact that he himself is an empty suit of armor helps him believe crazy stories more easily.

The Promised Day
During the time skip, Alphonse was in Reole for some time, helping to reconstruct the city and making plans with Hohenheim. He mentions later that during this time, his "visions" of the Door and his own body become more frequent, and he seems to be disoriented and weakened immediately after they occur. At some point during the time skip he leaves Reole with Winry to join up with Major Miles. Just before the Promised Day, Al, Winry and Major Miles pass through Resembool on a government train, and two Briggs soldiers help sneak Winry back to her home, where she runs into Edward.

Al's train departs Resembool, and later that night as he sits hiding in one of the cars he experiences a blackout, and reflects that he has to hurry and get his real body back before his soul seal wears off. Immediately after he is attacked by Pride and Gluttony; Al tries to run, thinking that he is "in no condition to fight now," but Pride captures him and Al blacks out once again.

While Al seems to see himself in the white place before the Door, and think his body is speaking to him, Pride 'possesses' him by manipulating his metal body like a hand puppet. Pride directs Alphonse's body to Kanama, a slum of Central, where Hohenheim is hiding and Edward has just arrived. Pride imitates Alphonse's voice and tries to separate Edward from Greed/Ling and the chimeras, but Ling senses Pride through the Xingese ability to "read the Dragon's veins," and briefly takes back control of his body to warn the others. Pride announces his plan to kill Greed and then bring Edward and Alphonse to Central. Thanks to some quick thinking and a few of Lan Fan's flash bangs, Edward manages to break Pride's control over Al. Darius then takes Al's body away from the fight, and he reawakens in his father's care. Alphonse seems to have been aware on some level that Pride was possessing him, since he immediately warns Hohenheim that Pride must be nearby, and after Hohenheim assures Al that he is now free of Pride's control, Al says that "it felt like Pride was interfering with my soul" and that it felt "disgusting."

While Edward and Greed continue to fight Pride, Alphonse comes up with an idea to trap the Homunculus using himself as bait, even though he "knew Brother would be against it." He and Hohenheim return to the fight, where Al feigns an angry attack at Pride, and the diversion allows Hohenheim to trap them both in an enormous earthen dome, where Pride will be completely powerless in the complete darkness. As Alphonse requires no oxygen, he would be safe in the dome, but expected to miss all of the fighting during the Promised Day, as there was no way to get him out without Pride escaping as well. Trapped together, Al argues with Pride about his humanness, and lets Pride play with his helmet.

However, Al's mild-mannered nature proves dangerous; Pride had actually been sending a Morse Code SOS by tapping on Al's helmet, and soon Kimblee arrives, nearly kills Heinkel, and frees Pride and Alphonse.

Taken by surprise, Alphonse is forced to destroy his own legs to escape Pride's grasp and then creates a dust cloud in which he tries to escape with a severely wounded Heinkel. Heinkel tries to convince Alphonse to leave him, but Al refuses; Heinkel then reveals that he still has the crystal-shaped Philosopher's stone that Kimblee lost in the mines of Baschool. Heinkel convinces Al that the souls within it want to help defeat the power that killed them. Using the Stone, Al gives a rare display of his powerful intellect as well as his fighting ability. He outwits and defeats Pride in a matter of moments and traps him in an earthen dome once again. Then Kimblee and Alphonse talk about the Philosopher's Stone, and Al suggests that Equivalent Exchange can be subverted and that good can be achieved without an equivalent evil. Kimblee scoffs at Al's optimism and reveals that he still has the spherical Philosopher's Stone.

Kimblee's explosion frees Pride, but Al once again proves he is several steps ahead; he lets himself be captured in order for Marcoh and Yoki, who have just arrived, to use the stone to heal Heinkel. Heinkel then attacks Kimblee and Yoki drives his car right into Pride, saving Alphonse and Marcoh. As they escape in Yoki's car, Pride cryptically states "Brave humans sure are easy to trick" as he watches them going away, hinting that they may run into a trap.

Yoki's poor driving delays them and they get into two accidents in Central before the four decide to run the rest of the way to Father's lair. They don't get far, however, before Alphonse is transported through the Gate directly to Father, along with Edward and Izumi. The experience induces the last of Alphonse's black-out visions; his metal body arrives in Father's lair where a panicked Edward, who has not spoken to Alphonse since the visions began, is unable to help, while Alphonse's consciousness is at the Gate with his body.

Alphonse's body (or perhaps Truth wearing Alphonse's body) asks him if he wants to return to how he was before, but seeing how weak and malnourished it was, he decides to return in his suit of armor so he can fight properly to protect his loved ones after realizing there was no way he could fight with his original form. His body mentioned after he left that he would have been proud to be his container but his return to the real world may bring nothing but despair and ruin.

Alphonse returns to consciousness in Father's lair as Edward, Izumi and May watch over him. Then while May tries to fight Father with Alkahestry, she tells the brothers to fight Pride. Alphonse and Edward, fighting together at last, face off against Pride briefly, but when Father's ability to transmute without moving proves too much for May, Edward tells Al to leave Pride to him. Alphonse rushes to May's side and protects her with his body while she partially heals herself.

The Final Fight and New Beginnings
After Hohenheim and the Xerxesian souls inside him stop Father's Nationwide Transmutation Circle and return the Amestrians' souls to their bodies, Alphonse, Edward, May, Izumi, Greed and Hohenheim face off against Father again, who now looks rather like Edward.

Father escapes upward out of his underground lair, and Al goes with Hohenheim, May and Izumi (leaving Roy with Riza and the chimeras) to follow him while Edward, at his own insistence, stays below to fight Pride. Aboveground, Father creates a huge explosion and Al throws himself in front of May to shield her. The impact leaves Al in ruins: He had lost his legs and his seal was slightly cracked. When Edward loses his mechanical arm and his left arm impaled on some rubble, Al does the unthinkable. With May's help, he transmutes his soul to exchange it for the return of Edward's original right arm. He is then seen with his body at the gate. Alphonse says he's ready now and all they can do is believe in Edward now; he shakes his body's hand and gains back his body at the Gate. Truth then asks Al if he thinks Edward will try to get him back to which Al responds he will. Truth then loses the arm he stole from Edward as he asks Al what he thinks that his brother will sacrifice to get Al back.

When Ed comes for Al, Ed sacrifices his 'Gate' for his brother. Al is suprised as being able to feel again and attemptes to readjust to normal life. In the end, he will travel to Xing to study alkahestry with May. Accompanying him are Zampano and Jerso, acting as bodyguards as well as searching for a way to return their bodies back to normal. In the epilogue, he is seen in a picture with Ed and Winry married and it is implied that he and May are romantically involved as she is seen in the picture with them. In a gaiden, it is revealed that Alphonse's armor was sent to them from Central, and, thinking of what to do with it, Alphonse decided to have it melted down to be made into automail parts to help anyone else it could out of a sign for respect. The helmet however, was salvaged by Den and used as a nest for some birdlings she found.

2003 anime series
After the dying Solf J. Kimblee uses alchemy to transform Al's armor into explosive material to get his revenge against Alphonse for previously humiliating him, Scar transferred all of his incomplete Philosopher's Stone into Al to save his life. As a result, Al became the Philosopher's Stone. Shortly after, Alphonse learns his body became lighter and his blood seal could endure contact with water. He also gained the ability to perform alchemy without a circle, although this is due to him "remembering" the gate. He only uses alchemy twice after he becomes the stone because any alchemy he or anyone near him uses activates the stone and destroys a part of Al's body. Because he houses the Stone in his body, he becomes the primary target of Dante's attempt to cheat death, but not before he becomes a pawn in Shou Tucker's plot to resurrect Nina. Once captured by the Homunculi for Dante, Al was to be devoured by Gluttony to complete the Stone inside Gluttony's body. But when he saw his brother killed by Envy, Al uses the stone's power to restore Edward's body (including his missing limbs) and re-bind his soul to it. This destroys his own body as he used up the whole of the Philosopher's Stone in the transmutations.

Alphonse becomes the Philosopher's Stone and regains full memory of his visit to the Gate. The concept of this is never fully ventured, due to his fear of the possible outcome effects of using the Stone's power. In the final episode of the series, he clearly uses alchemy without the need of any transmutation circle, in order to resurrect his dying brother. After Ed is revived, Ed performs one last transmutation on himself and sends himself to our world to pull Al's body and soul back to Amestris.

When Al came back to his body, he had forgotten his experiences in the armor and was physically the same age as when his body was taken away by the gate.

Conqueror of Shamballa
In the Conqueror of Shamballa, Al has grown into a powerful alchemist. He is first seen walking in the desert, where he transmutes a well to drink water. He eventually comes to Reole, just in time to save the town from the Thule Society's soldiers in armor suits. It is revealed that he still hasn't regained his memory of the past years, not recognizing Alex Louis Armstrong, however, he is determined to find his brother. As the suits of armor are sucked into the portal in the sky, Al manages to bind a part of his soul to one of them, having figured out that the portal leads to the parallel world where Edward is. Once the suit is on the other side, Al, who is able to see through it and control it, meets Ed, and is overjoyed to see him, but the two are forced to flee immediately as the Thule Society's troops start shooting. Eventually, after talking to Ed, Al's alchemy wears off, but not before he reassured Ed that they'll meet again. Later, Alphonse (with Wrath observing) prepares the circle to get the Gate open, but realizes that the sacrifice is needed. They are attacked by the powered-up Gluttony, who Wrath lures into the circle, letting him bite him and asking Al to open the Gate using both Homunculi as sacrifices. After the Gate opens, Thule Society begins their invasion of Amestris, and Al, having met up with Ed, sets out to fight its forces. With the help of Roy Mustang, they defeat Dietlinde Eckhart, however, Ed leaves to close the portal on the other side. After crossing the portal, Ed finds out that Al had managed to hide himself in a suit of armor almost identical to the one his soul had been bound to. After Alfons' funeral Ed and Al decide to find the atomic bomb and dismantle it.

Trivia

 * The character of Al bears some resemblance to Agilulf, the protagonist of Italo Calvino's The Nonexistent Knight. Like Al, Agilulf is nothing but a living suit of armor, a formidable fighter, and holds a sense of good manners.
 * Al was voted the fourth most popular character of the series in the recent fan poll.
 * In a manga extra it is shown that Al only allows women and cats into his armor, though the 2003 depicts him carrying Black Hayate (a dog) inside of him, and in chapter 56 he is also shown carrying Xiao-Mei (a panda) therein.
 * Al is one of two people in the series who knows Winry and Ed have romantic feelings for each other, the other being Riza Hawkeye.
 * In the manga/2009 anime, Alphonse; as a direct descendant of Van Hohenheim; is close blood kin to Father and all the seven Homunculi (though King Bradley can be a slight exception, as he is a human based Homunculus but nevertheless still shares the close blood kin to Al like the others). Additionally, Arakawa has jokingly confirmed that, in the manga, Al (along with Ed) is technically uncle to the seven Homunculi, as he relates to them by blood.
 * Al's breechcloth is white in the manga and 2009 anime, while in the 2003 anime, it's light violet.
 * In episode 12 of Lucky Star, a cosplayer is seen portraying Alphonse in full armor at Comiket.
 * Al makes a cameo appearance in Episode 5 of the anime series, Hayate the Combat Butler when he is referenced by Nagi Sanzen'in, who shares the same Japanese voice actress as him.Vlcsnap-2010-10-11-08h37m16s176.png
 * Alphonse has two theme songs on the Brotherhood anime CD: one, called "Kaze ni Dakarete" performed by his seiyu Rie Kugimiya, and one called "Restore Steppin'" performed by both Kugimiya and Edward's seiyu Romi Park.
 * Alphonse is named after the Comte Alphonse de Toulouse-Lautrec, father of the french artist Henri Marie Raymond de Toulouse-Lautrec.
 * In the manga and 2003 anime, the rectangular plate under the chin of Alphonse's helmet has five openings. In the 2009 anime, it has four, excluding rare animation mistakes where it is drawn with three or five.