Japan, 2077: A female agent named Vexille is dispatched to Tokyo to investigate whether Japanese are developing robotic technology, which has been banned by the U.N. due to its potential threat to humankind.

Edward Elric, the Fullmetal Alchemist, is on the other side of the gate. He has befriended someone who resembles his brother, Al, and has met a gypsy resembling Rose. He finds out that the Germans are planning on opening the gate, and attack the other side, which is Ed and Al's home. Although Al has learned a lot, he cannot stop all of them, and Ed cannot use Alchemy while in the other side. Ed tries to stop them, and Al just tries to be able to talk to his brother again, who everyone else thinks is gone.