While visiting with his subordinates in the hospital, Mustang admits to them that he now suspects that the homunculi were responsible for the Ishval Civil War to force someone to use the lives of the Ishvalans out of despair to create a Philosopher's Stone. Jean Havoc backs this up by stating that the military had been getting involved in a lot more conflicts since King Bradley took over as Führer. Mustang admits that the reason why he can no longer trust the Führer is because of his willingness to sacrifice innocent lives to secretly create the stone. Ed changes his hair color with alchemy, along with his clothes, while Al's armored body is hidden in a fake statue as disguises, and after saying goodbye to Winry and Sheska, the two depart to end the conflict over the Philosopher's Stone. Back at Dante's hideout, Hohenheim explains their souls are gradually eroding with each transfer and will soon lack the energy needed to maintain a body. Dante refuses to accept the truth, and reveals that while she used the last bit of their old Philosopher's Stone to transfer to Lyra's body, it does not matter because of Scar's actions that have turned Alphonse's body into the stone. He is then distracted by Sloth's resemblance to his late wife, Trisha Elric, and is trapped by her. Dante then uses Rosé’s baby as an alchemical key to open the Gate and banish him inside it. She then meets with Rosé, which makes it clear she plans to use her as her next host. She then frees Lust from her imprisonment and dispatches her to aid Sloth and Wrath in capturing Alphonse to bring the stone to her. She even states that she will fulfill her promise to turn her into a human if she succeeds.

Though their disguises on the train which hide their official records are effective, the Elric brothers are forced to flee when the military search threatens to destroy the statue Al is hiding in. Retreating to a nearby hotel, Ed leaves him to go do something. At Central Command, Mustang meets with Major Armstrong, where, having been recently promoted to Brigadier General and Lt. Colonel, the two are ordered to launch military operations across the border in the north to, nominally at least, capture the Elric brothers or force Drachma to send them back. However, Mustang reveals the testing of the Führer's reaction was part of his plan to verify what the Elrics said before about the Führer's identity. Since it gave Bradley away and exposed their secret communication with them, he believes that he will be murdered at the front lines to silence them for learning too much about the truth.

Ed meets Izumi Curtis at Dante’s house, who had been in hiding, to learn the secret behind her master and he asks her whether there is any part of her child’s corpse remaining, which would give him a weapon to use against Wrath. Al travels to an empty factory where Tucker is waiting for him, and he asks for his help in learning how to use the Philosopher’s Stone.