Fullmetal Alchemist the Movie: Conqueror of Shamballa

Fullmetal Alchemist the Movie: Conqueror of Shamballa is the first and only feature-length Fullmetal Alchemist film, and serves as the conclusion to the 2003 anime series. The movie is set two years after the series and takes place mainly in 1923 Germany.

Plot
Edward Elric, having been sent to the other side of the Gate (ending up in our world) at the end of the anime, is trying to find a way back to Amestris. Meanwhile, on his side of the gate, Alphonse Elric is trying to find a way to bring his brother, Edward, back home. Al has had recurring dreams that he is in Germany with Ed. During the two year time gap between the end of the series and the beginning of the movie, Ed has become a rocket scientist and is living with a boy named Alfons Heiderich, Al's "real-world" counterpart. They meet up with a group of gypsies headed towards the fair that Ed and Heidrich were going to to demonstrate one of their rockets. Edward saves one of the gypsies, Noah, from a group of men trying to capture her for her ability to read minds and runs off with her to safety. Later, soldiers from the mysterious pro-Nazi secret society known as the Thule Society, tainted and crushed, appear in Lior, and are quickly dispatched by Al in his original body. He realizes that they have come from another world and has to be the portal to where Ed is. Al uses Soul Transmutation to transfer part of his soul into a suit of armor, that ironically looks like the one he wore in the series.

Meanwhile, Ed and Heidrich are keeping Noah at their apartment. In the city, Ed sees a man drive by that looks like Führer King Bradley. After confronting him, he realizes he isn't Bradley, but his counterpart, a Jewish movie director named Fritz Lang. He is searching for a dragon to use as inspiration for one of his movies. At first skeptical, Ed joins the search at an abandoned castle where the dragon was last sighted. He finds the dragon, which turns out to be Envy in the form he took in the last episode of the 2003 anime. Soldiers from the Thule Society come in and apprehend Envy to use in their experiments. Back at the Thule Society head quarters, Envy is strung in a circle above a large Transmutation Circle like image, and after biting into Hohenheim, activates the circle with his blood, sending the soldiers into the gate and to Liore.

Later, Ed breaks into the Thule Society head quarters and after finding the room with the circle, fills it in properly and accidently activates it with his blood from a cut on his face he sustained from a piece of glass when entering the society. This opens the Gate and sends the bodies of the soldiers who went in before, along with Alphonse who sealed part of his soul into one of the suits of armor during the fight. After a brief reunion, the two proceed to escape the society. Al can't keep his soul attached to the armor for long, so his soul dissipates and escapes soon after. This is enough time for the brothers to confirm that they had accomplished their goals from before.

During this time, Winry had traveled to Dublith and discovered that Izumi had succumbed to her injuries from human transmutation and died. At her grave, she finds a disheveled Wrath and takes him back to Resembool for automail maintenance. There, he confronts Alphonse and leads him to the underground city. They are attack by a deformed, monstrous Gluttony and, after a battle, Wrath traps him and Gluttony in the transmutation circle Al had made to open the gate. Al activates it and uses the two Homunculi as sacrifices. In front of the Gate, we see a brief scene of a naked Wrath reuniting with a naked Izumi and the pair going into the gate together.

While this is happening, Noah is contacted by the Thule Society and is told to read Edward's mind and find out how to activate the transmutation circle. At the beer hall, Ed and Noah go for dinner, but find that every one within the hall, including Hughes' counterpart, is a member of the Nazi party that is planning to overthrow the German government. Before Ed can be captured, Fritz Lang breaks through the wall and rescues Ed, who proceeds to fly to the Thule headquarters and break through the window into the room with the Transmutation Circle and Heidrich's finished rocket, which is prepared to fly soldiers into the Gate and conquer Amestris. Dietlinde Eckhart, the leader of the Thule Society, was planning to use the technology and resources in Amestris (which she thought to be the mystical Shamballa) to conquer the world. Ed is about to attack her but stops when he sees Hohenheim in Envy's mouth. He proceeds to apologize to Ed for all that he has done and, after asking him to give Al his regards, forces Envy's mouth down on him and uses his blood and Envy's body to open the Gate.

While he is distracted, Eckart shoots Edward in the prosthetic arm, who falls to the area containing the rockets. He wakes up to find he is strapped into another rocket created by Heidrich. As he launches off, Heidrich is shot by a member of the society and dies, happy that he has done something that matters. On his way into the Gate, Ed sees Noah who asks him to take her with him, but leaves her anyway. On the other side of the Gate, Ed crashes in the underground city and finds Al, Winry, and Sciezka there. After a brief reunion, they see Eckart and her fleet of ships, who had previously been mutated by the Gate Children, fly into Amestris. Al is horrified that he let something like that into the alchemic world and runs off. Ed tries to follow, but his broken automail prevents him from it, and Winry quickly installs a new arm and leg to Ed while several more ships pass through the Gate. Ed finds Al about to try to transmute a child who had been crushed by a collapsing house, but Ed stops him and tells him they need to stop Eckart. Al agrees and they both set off to attack the war ships.

At the Central Command, soldiers are barely fending off the attacking soldiers of the Thule Society with Major Armstrong, until Roy Mustang arrives and attacks several of the soldiers with alchemy. After giving orders and mobilizing soldiers, he creates a hot air balloon to directly attack the war ships. After taking to the skies, Roy Mustang then meets up with the Elric Brothers to take down the main ship. Fighting through most of the ship's external defenses and boarding the ship, Mustang remains outside to secure the only exit whilst the Elrics enter to fight Eckhart, who can now use alchemy. After Eckhart briefly fights Edward, she then retreats and releases several armored Thule Society solders to finish him, but they then turn on her due to Alphonse previously placing parts of his soul within the suits. Edward and Alphonse then flee, but Edward then uses alchemy to send Alphonse and Mustang back to the ground without him, despite Al's objections. Before Alphonse leaves, Edward instructs Al to destroy the portal in Amestris while he destroys the one beyond the Gate, so that they can prevent any further invasions.

Edward then pilots the ship, and flies it back through the portal, crashing it in the lab containing Noah, cradling a bloody Alfons. Upon exiting the ship, Ed finds that a suit of armor similar to Al's begins to talk - but when he inquires how long until the soul fragment fades, he finds Alphonse within it, who states he climbed back onto the ship after telling Mustang to destroy the portal in Amestris. Eckhart then leaves the ship, covered in Gate Children, and is killed by Officer Hughes. The brothers then decide to dismantle the portal together, despite not being able to use alchemy.

After attending the funeral of Alfons, the Elrics and Noah then ride in a vehicle which contains multiple travellers (driven by the real world versions of Lust and Scar). The brothers decide to destroy the Uranium bomb, and choose to continue to live in their new world, regardless of rumors of a "second great war", as Earth has become their new home.

Trivia

 * The film takes place in a peaceful, yet shaky time in our world. 1923 Germany was being riled with reparations payments from the Treaty of Versailles that ended World War I, which caused a revolutionary mood in Germany, whose citizens were most unhappy. This is best represented by the fact that at the very end of the film you see a man who is quite obviously Adolf Hitler being arrested for attempted overthrow of the Weimar government; a reference to the 1923 Munich Beer Hall Putsch.
 * This film also depicts the rise of Adolf Hitler and the rise of the Nazi Party, which will start World War II in 7 years.