Edward enters the depths of the 5th laboratory. There, he learns that it was used as alarge-scale biological research facility to find military applications for alchemy. In the laboratory lies an enormous amount of incomplete Philosopher's Stone left over from that research. Tucker had intended to use those materials for Nina and proposes that Edward complete the Philosopher's stone.
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Hughes is woken up by Mustang who comments that he has not appeared on screen in awhile. In their conversation, Hughes chooses not to mention the events surrounding the Elric brothers. In order to protect the brothers, he authorizes a search of the interior of the 5th Laboratory but warns Mustang, Bloch, and Ross to prepared for any punishment they may receive.
Back at the lab, Scar and Al desperately fight for their lives.
Through the examination of documents provided by Tucker, Ed realizes that the lab was for researching military applications of alchemy while focusing on organic transmutation using the Philosopher's Stone.
As Hughes and the others rush to the 5th Laboratory, they are stopped by the Fuhrer who will personally accompany them and let the Major command a battalion of soldiers as well.
In the lab, Lust sits atop a captured Al while Gluttony returns and reports that he has dropped Scar into a place he cannot go. She wishes for Ed to hurry up before he is interrupted by Greed.
Ed heads to the room above the transmutation circle and is told by Tucker that it acts as storage tank to supply the bottom room. Unknown to him, Envy, disguised as Gran, is just behind the wall and within the storage tank are tens of human prisoners.
Ed, back in the main room, states that if he is successful in creating the Stone, he will give Al his body back and then disappear forever.
Above, the Crimson Alchemist creates an explosion using a fellow prisoner and combined with the red water creates a hole which all the prisoners fall through. Ed is shocked to find out he was about to transmutate so many human beings. When he asks who brought them here, Envy answers but is quickly interrupted by Ed's attack.
Envy capitalizes on Ed's dysfunctional arm and beats him to the ground. However, Envy is stopped by Lust who asks Ed to continue the transmutation, for the ingredients are all there.
Using Al as leverage, Lust and Envy force Ed to fix the ceiling and start the transmutation. It it then that Ed discovers the true intention of the Homunculus. All they want is to become human; that is why they seek the Stone. Lust proposes a trade: she will tell Ed how to create the Stone and Ed will use the Stone and turn them into humans.
Just before he can complete the transmutation, Ed is interrupted by Scar who tells Ed to protect his little brother as an older brother is supposed to do. On his way to get Al, Ed steps in a pool of red water and a massive reaction ensues. He launches a massive attack that drives away Lust, Envy, and Gluttony.
The raiding party organized by the Fuhrer storms the laboratory to rescue the Elric brothers. One of the parties is met by the Crimson Alchemist and destroyed by Greed's subordinates.
Armstrong, Ross, and Bloch arrive at Ed's location only to find Ed's transmutation reaction cascading infinitely. In order to save Ed, Ross walks up to Ed and embraces him.
Lust, Gluttony, and Envy escape and are complemented by the Fuhrer's secretary for their good work. Soon after, Armstrong emerges with the Elric brothers under his arms.