Each of the Elric brothers finds himself in fierce battle with a guard of Laboratory 5. However, both brothers soon discover that the guards are identical to Al; the guards are souls bound to empty suits of armor. Number 48 reveals himself as Slicer, a serial killer, and Number 66 reveals himself as Barry the Chopper, who the brothers helped arrest. Though Ed feels his auto-mail failing, he manages to grab Slicer's helmet, immobilizing Slicer. However, Slicer reveals that he was in fact two brothers and the suit of armor continues to attack. Remembering his goal, an exhausted Ed finally disables Slicer. The Slicer brothers ask for death, calling themselves inhuman, but Ed refuses because it would force him to admit that Al isn't human either. Outside, Barry the Chopper is stunned to find that Al is a suit of armor as well. However, he manages to convince Al that Al's personality and memories were all fake implants, and remembering the question that Ed failed to ask in Resembool, Al begins to wonder.
Ed and Al are horrified by the "truth behind truths" Marcoh's notes revealed about the key ingredient in making a Philosopher's Stone, and nearly give up their quest. Al tries to convince Ed to continue, but it is Maria Ross who inspires him to continue. Wanting to ascertain the truth for themselves, they decide to investigate Central's Fifth Laboratory, suspecting that the lab, officially closed for years, is secretly being used for research on the Philosopher's Stone. Ignoring the orders of Ross, they sneak out to investigate the laboratory themselves. Ed sneaks in via an air duct, leaving Al alone outside. Searching for Ed, Scar attacks the dormitories and gathers that the brothers have traveled to the Fifth Laboratory before the military apprehends him. Inside the lab, Ed triggers several traps before finally meeting Number 48, who declares his job as the laboratory's guard and attacks. Outside, a similarly dressed guard named Number 66 attacks Al.
In the library in Central City, Lust and Gluttony search for Marcoh's research. Scar, also looking for Marcoh's research, notices that Lust reminds him of someone he knows. When the pair attacks him however, he realizes that they are Homunculi. Returning from Resembool, Ed and Al arrive at Central by train and meet their new bodyguards, Maria Ross and Denny Brosh. When they arrive at the National Central Library, 1st Branch it is a smoldering mess and Ed and Al go on a exhaustive search to find other sources for the book. Hughes, reporting on the Library's destruction, notes that Scar was present, though he was probably fighting somebody. Ed and Al's search leads them to the house of a librarian named Sheska, who they find trapped under a pile of books. After they save her, she completes a report on the exact contents of Marcoh's document. The brothers work to decode it and discover that the Philosopher's Stone requires human lives.
Ed and Al return to Resembool with Armstrong and are greeted by Pinako. Winry, appalled by the damage sustained by the brothers, admonishes the pair. Pinako, understanding that the brothers need to return to Central urgently, agrees to repair Ed's arm and adjust Ed's leg in just three days. Armstrong, refusing to rest like the brothers are, helps out and tells Pinako and Winry about the Elric brothers' fame. Ed visits his mother's grave and both of the brothers reminisce about their childhood. While measuring Ed, Winry notices Ed's silver watch and becomes infatuated by it, but Ed refuses to let her dissemble it. When Ed and Al go upstairs to sleep, Al reveals that he is worried because of his fading memories, but Armstrong breaks the tension. A few days later, Ed has his mechanical joints reattached and is temporarily debilitated. When he regains his movement, he fixes Al and the two spar. Winry takes advantage of Ed's absence to investigate the watch. After the brothers finish sparring, Winry returns it to Ed in tears over the brothers' seeming lack of emotion. Ed and Al depart on a walk, telling Armstrong about their childhood. After the night, they depart and Winry and Pinako wish them a safe trip.
Ed and Al head back to Resembool to repair Ed's broken arm and Al's broken armor, and Armstrong volunteers to tag along to protect them. Lust attacks Marcoh in his "safe house" and coerces him into revealing the location of his research on the Philosopher's Stone. She, along with Gluttony, then kills him and heads toward the National Central Library, 1st Branch. On the train to Resembool, Armstrong and Ed discover that Al was unloaded at the previous station and are forced to search for him. When Armstrong urges patience, Ed explodes in rage and abandons Armstrong. However, Ed is jumped and his leg is stolen by a young girl. The girl's grandfather explains that he lost his leg during the Ishbal rebellion and that he wishes to retain his wound as a reminder of it and returns Ed's leg. Al, stolen by a boy who wishes to prove himself by raiding an enemy's mansion, scares the boy out of the attack by claiming he is a haunted armor. Ed and Al reunite and Armstrong reappears. Grabbing the brothers, Armstrong dashes toward the departing train hoping to catch it.
