The Evangelion saga from TV is artfully recounted, with some additional scenes, in part one see: "Shin Seiki Evangelion" (1995) Part two starts immediately afterward, where the NERV organization has outlived its usefulness. The shadowy covenant of SEELE launches an all-out commando assault against the ill-defended headquarters. Asuka, semi-comatose, is placed in her EVA for safety, while Misato and company struggle to find Shinji and Rei before they're assasinated by SEELE's forces.

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.