With the mysterious boy who possesses the tatoo of the homonculus at the center of things, a confrontation occurs at the South Headquarters. Edward, Izumi, The Lizard Guy, the Mad Bomber, as well as the Military find themselves facing off against each other. On the other hand, the Fuhrer orders Colonel Mustang to lead a troop of men to apprehend Scar in the rebel slums.
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Mustang and a large contingent of soldiers board a train headed to Kishua City's west slum where Scar is believed to be hiding out. Aboard the train, Mustang's subordinates express their concern regarding the upcomming mission.
Back at the slum, Scar seems to have disappeared, but he is still in examining the tattoos on the wall. A man enters and is frightened by the similarities between the tattoos on Scar's arm and the ones on the wall.
At the crumbling South Headquarters, the five groups face off against each other in a battle royal. Quickly, Ed has the wind knocked out of him by Izumi, but she is halted by Al. In the meantime, Envy, disguised at the Fuhrer, swoops in and snatches the child.
Izumi's attempt to save the child is thwarted by Armstrong who begins to fight with Izumi. She easily out classes him, and he is only a hindrance to her goal. Attempting to intervene, Ed and Al are taken on by the Crimson Alchemist and the lizard man.
Ed asks why they are interfearing, and the lizard man replies that they also want the child and their boss has business with Ed and Al.
In the basement, Envy transforms back to his original form and confronts the child. Telling him that he is no longer alone, Envy feeds the child incomplete pieces of the Philosopher's Stone while explaining to him that the stones took human lives to create.
Even though he is shocked, he cannot resist the taste of the crystals and devours them. Envy is surprised that he can do alchemy and also explains that they are not human.
Unable to handle the situation, the lizard man and Kimbley escape from the South Headquarters, but not before Archer gives Kimbley his proposition. Archer can arrange for Kimbley to return to the military.
Ed and Al dash through the building looking for Izumi and stumble upon Armstrong who has been defeated by her. Elsewhere in the building, Izumi has found the child and run off. Unable to find Izumi and forced to escape because they are trespassing, Ed and Al return to the butcher shop where they as Sig Izumi's whereabouts.
In the control room of the South Headquarters, Archer is shocked to find that the Fuhrer had no plans to come south for an inspection. Armstrong enters not having accomplished his mission because he believed that the security of the building was more important.
At the butcher shop, Winry tells Ed that Izumi went to Yokk Island where she attempted to revive her child's body.
On the island, the child's complexion seems to have changed from his encounter with Envy. She holds his neck wanting to kill him but is unable to finish the task. Instead, he chokes her until Ed intervenes.
She explains to Ed that it was her who created him when she attempted human transmutation. Instead of the gate being a source for obtaining the truth, she feels across that gate lay hell.
The child explains to Ed that Homunculus are created when humans attempt human transmutation. They create a being with a body and a mind but no soul. He goes on to explain that Envy and the other Homunculi were also created long ago thanks to the idiots who attempted human transmutation. It is for that reason that they all wish to become human.
Mustang and his contingent of soldiers arrive at the slums while Sloth speeds towards Yokk Island. On the island, there is a confrontation between Greed and Envy, but Envy is forced to retreat with the arrival of Sloth.
Izumi's child turned Homunculus is now known as Wrath by the other Homunculi. Sloth reveals that the original plan was to use Wrath as bait to push Ed towards the Philosopher's Stone. However, Envy wants to see Ed's face tremble in fear.
Wrath explains that only after Ed put his arm and leg across the gate was he able to get out.
Unable to fight, Ed is protected by Al who will fight in his place because they have journyed too far to just give up now.