In the wake of the battle against the third angel, a catastrophic event occurs, causing Unit-01 to go berserk. During this frenzy, Shinji’s consciousness is mysteriously expelled from his body, leaving him in a state of complete amnesia. As the battle rages on, Unit-01's true nature is revealed as it acts on its own, leaving Shinji blank.

Shinji wakes up in the NERV hospital, surrounded by unfamiliar faces. He is disoriented and unable to recall any memories except for his own name.