Edward is in a state of pain; he regrets that he was unable to save Nina. He looks back upon his helplessness and regrets his hesitation. Lt. Colonel Mustang orders Edward to begin the analysis of Tucker's research. However, Edward refuses and instead, begins to investigate the serial murders that may be related.
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Ed is distraught over Nina's and Alexander's deaths. However, Mustang tells him that in order for Ed to accomplish his goal, he must learn to move on even if he must force himself to do so.
While Ed and Al try to cope with the deaths of their friends, the brothers are ordered to organize Tucker's research in order to gain an understanding of what he was doing. In essence, Ed is asked to take over Tucker's research now that Tucker has been executed.
It is during this process that Al stumbles upon research regarding the Philosopher's Stone. Trying to rebound from Nina's death, Ed volunteers to help find the serial murderer but is turned down by Mustang. Angered by Mustang's attitude, Ed turns in his pocket watch and decides to investigate the matter by his own hands.
Even though Al seems more level headed about the situation, Ed is unwilling to listen and runs off. In his time alone, he meets the man from the library who tells him that he is better off not being a State Alchemist.
Meanwhile, Winry has arrived by train to congratulate Ed on his achievement.
In Ed's absence, Al has gone about inquiring about the Philosopher's Stone. While Hawkeye shys away from the topic the Fuhrer offers what information he has about the Stone. At the cafeteria, Ed and Hughes discuss clues regarding the serial murder case.
While waiting for Ed outside, Winry is drawn to a refrigeration machine. When Ed gets there, all that is left are Winry's bags. Connecting the dots, Ed deduces that Winry has been kidnapped by the serial murderer and dashes off.
Finding the refrigeration car, Ed enters the slaughterhouse only to be knocked out by the murderer. When he awakens, he finds his right arm missing and is introduced to Barry, the shop's owner. As a reward for tracking him down, Barry shows Winry tied and gagged to Ed.
With a screw he picked up earlier, Ed draws a transmutation circle and frees himself only to be attacked by Barry. While Winry watches in horror, Ed scrambles around on the ground avoiding Barry's deadly slashes. After painfully reinserting his right arm into its socket, Ed helplessly tries to defend himself.
Stopped by Al right before he can kill Barry, Ed slashes blindly only to find Al standing there before him. Truly shaken, Ed is confronted by Al as Barry is apprehended.
Brought back to reality by his close encounter with death, Ed decides with Al to search for the Philosopher's Stone that has the potential to make their dreams come true. However, in order to gain access to the military's information about the Stone, Ed must become a State Alchemist once again.
Ed is reinstated as a State Alchemist under the condition that he is given access to information regarding the Stone and allowed to search for it when not on a mission. Accepting these conditions, Mustang hands the pocket watch back and gives Ed the name of Full Metal Alchemist.