Concurrent theatrical ending of the TV series "Shin Seiki Evangelion" (1995). After the defeat of the final Angel, Shinji Ikari falls into a deep depression. When SEELE orders the JSSDF to make a surprise attack on NERV's headquarters, Gendo Ikari retreats down into Terminal Dogma along with Rei Ayanami, where he begins to advance his own plans for the Human Instrumentality Project. Eventually, Shinji is pushed to the limits of his sanity as he is forced to decide the fate of humanity.

A recap of the first 24 episodes of Neon Genesis Evangelion, followed by a 30-minute continuation of the plot that would later form the first third of The End of Evangelion. 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.