After escaping from Central Prison, the Freezing Alchemist, Isaac McDougal, sets his plan in motion to kill Führer King Bradley. However, under the command of Lt. Col. Roy Mustang, the military and State Alchemists attempt to stop him.

Ed is now in a hospital recovering from his wounds and Al is unable to let go of what Number 66 told him back at the Fifth Laboratory. Meanwhile, Winry agrees to make a trip to Central in order to repair Ed's automail... again!

When the conspiracy surrounding the Philosopher's Stone closes in on the highest ranks of the military, one of Mustang's most trusted and cherished allies is murdered.

After learning of Hughes's fate, Ed and Al are ravaged by sadness and guilt. Envy still hides in plain sight among the State Alchemists, and another Homunculus is on the verge of infiltrating their ranks as well.

Mustang must make a difficult choice: will he break alchemy's greatest taboo? Or will he watch the person dearest to him die? Meanwhile, it grows ever more difficult to discern where Ling ends and Greed begins.

As one shared journey ends, many journeys begin. Those most touched by the conflict which surrounded the Philosopher's Stone now go their separate ways. One thing is certain: they will meet again.