The one with the orange fur made the most appearances; he was first distinctly seen sneaking in the train that was supposed to transport Julia but she wasn't there as it was a trap orchestrated by the Amestris military. After a K-9 unit found out he wasn't human despite his disguise, he killed the dog and the soldiers which created a commotion. He transformed and soon had to face both Atlas and Edward on the train's roof. Furthermore, the Black Bats, a Milosian independentist group was also there for Julia. The situation proved difficult to handle and he had to retreat.
He was later seen having followed Julia, Atlas, Ed, and Al down to the bottom of the valley where the Black Bats and the Milosians live.
Before entering the tunnels that serve as the Black bats' HQ, he went through Ed and a member of the Black Bats. They tried to fight him but he didn't pay them much attention, only attacking them once each as he raced to the entrance: Ed managed to parry the claw but the soldier wasn't so skilled and died.
He rushed through the tunnels, dodging the bullets that were shot at him and tearing through the soldiers with ease but stopped and turn around when he had enough of Ed stalking him.
Ed told him he was going to pay for the man he killed before entering the tunnels (never-mind the others he tore apart on his way inside (note: they will also be forgotten at the burial later that day somehow)) as the Full-metal sentimental had grown attached to him.
They were then joined by Atlas and Alphonse. The werewolf chimera went to attack Atlas but was shot at by soldiers. He got rid of them by kicking a barrage of pebbles in their general direction but Julia, who wasn't aware he didn't want to hurt her and wanted to defend her group, shot him too. He was forced to throw some pebbles at her too because it's such a bad-ass way to deal with trained soldiers with rifles. Atlas went in the way and shielded her from the barrage by destroying it with Alchemy but hidden in the pebble was a lamp and it started a fire.
As Atlas got rid of the fire, the chimera flanked them, disarmed Julia and protectively placed his arm between her and Atlas. He told her to come along quietly and no one would get hurt.
Raul didn't learn from the other's mistake and tried to shoot him which earned him a pebble in the arm, but the shot was fired on a blunt stalactite above Julia and the werewolf chimera and it fell on them. The chimera managed to catch it to protect Julia. Alphonse used the opportunity to grab her away from him and as he got rid of the boulder on his shoulder and went to follow them, he was interrupted by Ed's building a pillar cage around him. He sliced the pillars easily and was faced by Ed and Atlas again. He dodged several of the latter's attack and dashed at him but before he could tear him apart or before Atlas could try to defend against the attack, he was restrained by some more pillars created by the Full-pillar Alchemist. Atlas used the opportunity to kill the bound chimera in a way that must have been horribly painful as his Claws literally popped off his fingers. The chimera upon death returned to his human form.
Two others, one with red fur and one with yellow fur were released by Colonel Herschel during the fight and arrived in the tunnels moments after the orange one's death.
The group managed to escape them by diving into an underground waterhole. As the two werewolf chimeras lost their scent, they had to retreat.
They wouldn't be seen again before the final fight, when they appear at their master Colonel Herschel's side as he was just revealed to be Julia's brother, and that he had been appointing the Werewolf chimeras to protect her as well as his plan to bury the Valley, to create more philosopher's stones and change the world.
He then sent them at the Elric brothers in an attempt to prevent them from helping his sister save the Valley from lava. After a short face to face talk with his sister, however, he pulled some magma from the ground and the two chimeras jumped away from the attack as the brothers and Julia shielded themselves with alchemy.
They landed behind Colonel Mustang and ended up both having to face him. It turned out all too fast for Roy, who just had to "put the wolfs meat on the rotisserie".
What is interesting to note is that first they weren't roasted to the bone and even still had fur on which indicates a rather small amount of damage made to the skin and the one already lying on the ground when the other one was shown roasted and losing consciousness, didn't revert to his human form like the one with the orange fur when he was killed.
This might imply that Roy didn't kill them or that roasted tissues can't revert.