Second Lieutenant Havoc explains to two soldiers how Colonel Mustang is able to create fire with a single snap. Later, in Mustang's office, Edward mentions to the Colonel that he wishes to know more about bio-alchemy, so Mustang introduces him to Shou Tucker, the "Sewing-Life Alchemist," who was able to create a talking chimera. While researching through Tucker's books, Edward and Alphonse become close with Nina, Tucker's young daugher, and her dog, Alexander.

Meanwhile, Tucker is facing his oncoming assessment date, and if his research isn't impressive enough, he'll lose his State license and funding. The stormy day before Tucker's assessment, the Elric brothers come to his home to study and he shows them a new talking chimera he has just created. When the chimera calls Edward 'Big Brother' he puts two and two together with the information he has on the coincidence of Tucker's wife leaving him two years before, and the creation of his first successful talking chimera occurring around the same time, and the fact that both Nina and Alexander are now nowhere to be found.

Confronted with this information, Tucker sets off Edward by telling him they're just the same in the way they have played around with people's lives. Edward beats Tucker severely and Alphonse has to stop him from killing Tucker. After Tucker's doings have been reported, Mustang chides Edward for being depressed over something 'so small.' Ed emotionally responds that a human life isn't small and that they're pathetic for not being able to save a little girl. Mustang tells him to go home or he'll catch a cold.

Back at Tucker's home, where he is under house arrest, a strange man makes his way past the outside guards into Tucker's room and placing his hand over Tucker's face, kills him somewhat explosively. He also kills the Nina chimera, as there is no way to restore her back to normal. He says a prayer for their souls and leaves quietly in the rain, while across town Edward lays awake in his bed.

Edward has a nightmare about his mother and unable to go back to sleep, he and Alphonse head off in the early morning to headquarters to find out what's going to happen to Tucker and Nina. First Lieutenant Hawkeye tells them that they were murdered during the night and that she's on her way to help find out who the culprit is. At the crime scene, Lieutenant Colonel Hughes and Major Armstrong look over what remains of the bodies and conclude that the killer is Scar, a man also responsible for the deaths of ten other alchemist in Amestris, five alone in Central.

At the same time in Liore, Gluttony and Lust look on from a balcony as chaos abounds below them. What appears to be Father Cornello joins them in conversation of how they were able to turn the townspeople against the military with their propaganda and how they suppose a lot of them will die. Brother Cray sees Cornello shapeshift back into the homonculus known as Envy, and they let Gluttony eat them so no one will find out. While Gluttony feeds, Lust and Envy discuss how since they're done in Liore, they'll move on to East City to take care of Scar, who has gotten in the way of their plans again.

Back at the crime scene in East, Detective Hughes mentions that he heard Scar had killed Brigadier General Grand the "Iron-Blooded Alchemist," who was a military martial arts expert and advises Colonel Mustang to increase his security just to be safe. Mustang suddenly asks where the Elric Brothers are and Hawkeye tells him she saw them walking down main street. He orders a car to go pick them up. The man Mustang sends for them finds Edward and Alphonse sitting in front of a clock, reflecting on their alchemic teachings.

It just so happens Scar is walking by at that particular moment, and hearing Ed's name, approaches them, killing the officer as he tries to protect them. The brothers flee, running to a nearby alley, and Alphonse seals off the entrance, thinking that will keep Scar at bay, but he simply blasts through it with his hand. The Elric's try to run again, but he blasts the wall, trapping them in front of him. Edward transmutes a pipe into a sword and the brothers prepare to fight Scar, but they're slower than he is, and he blasts Al's right side as he passes, and is quite surprised when it doesn't kill him. He is even more surprised when he doesn't damage Ed's right arm, and is discouraged by how long it is taking to dispose of them since his body-disrupting attacks have no effect on Al, and none on Ed's automail.

Alphonse begs Edward to run away because he can't help him, but Ed transmustes a blade onto his right arm and lunges at Scar. By this point Scar has figured out how Edward uses his alchemy and makes it a point to destroy Edward's automail arm, sending him into momentary shock.

Edward falls to the ground in pain in front of Scar, and he and Alphonse realize the severity of the situation. Scar tells Edward he'll give him a moment to pray, and Ed spits that there's no god he feels like praying to. He makes Scar promise that he won't touch Alphonse, who is begging for Ed's life and just as Scar is about to lay his hand on Edward, Colonel Mustang arrives and fires his gun into the air to stop the scene.

He explains to Edward that Scar is the man responsible for killing Tucker and Nina and that he's been killing alchemists all over the country. Scar insists he is doing the will of God as alchemists "change the natural into the unnatural." Mustang reveals that he too, is a State Alchemist and Scar turns on him to attack, but Lieutenant Hawkeye trips the Colonel and shoots at Scar just as he reaches them, reminding Mustang that he can't create fire in the rain.

Scar announces that he will continue to kill State Alchemists as well as their sympathizers, and Major Armstrong challenges him by throwing a punch, which Scar barely dodges. They battle each other, tearing up the street around them, and Armstrong reveals that Scar's attacks are alchemically based, and backs him into a corner, preparing to punch once more, but pulls back at the last second so that Hawkeye can fire a shot into Scar.

She only grazes him, but the sunglasses he's been wearing this whole time break, and his red eyes are revealed. Those eyes and his dark skin are indications that he is from *Ishbal.* Scar accepts that he is outnumbered and blasts away the ground, escaping through the sewers. As soon as the coast is clear, Lieutenant Colonel Hughes appears. Edward rushes to Alphonse to make sure he is alright and is met with a punch to the face from his younger brother, infuriated that Edward would roll over and accept death like he nearly did. Havoc picks up Al and all his pieces, and along with Lieutenant Hawkeye escorts the Elric's safetly away.

Colonel Mustang recounts a short history of the people of Ishbal and the civil war that took place there thirteen years before where State Alchemists were used as weapons to control the chaos, and admits that he was one of those alchemists, so he understands why one of the last remaining Ishbalans would seek justice. It is still understood that Scar is too dangerous to remain alive and the next time they see him, they'll kill him. Hughes asks Edward what he and Alphonse will do the way they are, and Edward says he needs his mechanic to fix his arm so that he can repair Al using alchemy.

Major Armstrong accompanies the Elric brothers on their journey back to their hometown of Resembool. Alphonse must ride in the baggage car, and is very sad to be treated like luggage. Before the train departs from the station, Lieutenant Colonel Hughes sees them off. As the train is pulling away, we see that Lust is aboard as well, unbeknownced to Edward and the others. At a stop in a small town on their way home, Major Armstrong sees Dr. Marcoh on the platform and calls out to him, but Dr. Marcoh hurries away nervously. When Edward hears that Marcoh is an Alchemist who used to study the use of alchemy for medical purposes, they exit the train to see if he knows anything about biological transmutation. Lust expresses intrest in Dr. Marcoh as well from the darkness.

After questioning some of the town residents, Edward learns that "Dr. Mauro" is the town doctor and has been treating people using alchemy. Major Armstrong explains to Ed that when Marcoh disappeared, he took some Top Secret documents with him as well and must have been hiding under and alias and thought they had come to take him back, so he ran. When they arrive at his house, Dr. Marcoh greets them at the door with a loaded gun, and after disarming him tells them why he ducked out of the military and that the research he took with him involved his attempts to create The Philosopher's Stone. He then shows them his incomplete form of it, which Ed realizes is what Cornello's ring was made out of.

When Edward asks to see his data and research, Marcoh scolds him for not understanding what he's getting himself into, and even when he realizes that Ed and Al have attempted human transmutation, he still refuses to let them see his data, insisting it is "the work of the devil." Edward and the rest return to the train station to wait for the next train to Resembool, and Dr. Marcoh suddenly appears at the platform with the location of his data, having reconsidered, and enigmatically expresses hope that Edward might be able to see "the truth that lies within the truth."

Dr. Marcoh returns home to find Lust waiting for him. We learn that she helped show him how to create the Philosopher's Stone, and she tells him that if Edward sees the data it could be bad. As he goes for his gun, Lust stabs him in the shoulder with her elongated finger to try and torture the location of Marcoh's data out of him. Marcoh refuses and transmutes a spike out of the wall, having used his blood to draw a transmutation circle, impaling Lust. However, Marcoh looks on in horror as her wounds heal themselves. At that moment, a young girl bursts through the door, her arms full of flowers, and is trapped between two of Lust's deadly fingers. Marcoh is forced to give her the location, which Edward is reading is the First Branch of the National Central Library.

Happy with her newfound information, Lust leaves Marcoh and the girl unharmed, but not before threatening to wipe the small town he lives in off the map should he leave it or try to get in her way. She is off to destroy the data before Edward can get his hands on it.