Shinji wakes up in the hospital, with no memory of defeating the Angel the night before. Rejected by his father, Misato decides to take Shinji with her to live in her apartment. Later that night, memories of the battle against the Angel come flooding back to Shinji.

Asuka joins Shinji’s class at school, and moves in with Misato and him in their apartment. As Asuka adjusts to Japan (or rather, everyone else adapts to her...), a new Angel attacks which is capable of splitting itself into two identical copies. EVA-01 and EVA-02 are defeated, and NERV is publicly humiliated. With the Angel in a week-long regeneration period after an N² Mine attack by the JSSDF, Asuka and Shinji must learn to "synchronize" with each others movements combat, in order to defeat it once and for all.

In the first half of the episode, a clip show is presented to the Human Instrumentality Committee of Seele, reviewing the attacks of all Angels up to this point. The second part includes a poem in which Rei contemplates her own existence, and a cross-compatibility test between Rei's and Shinji's EVAs.

Enraged over Touji's near-death at the hands of his own EVA, Shinji refuses to pilot an Evangelion again and prepares to leave Tokyo-3 for good. He is forced to reconsider that decision when an immensely destructive new Angel attacks just as he is about to leave...

Too frightened to face Misato or Rei, Shinji runs away yet again, only to meet and strike a friendship with Kaworu Nagisa, the replacement pilot for EVA-02. Kaworu's openness and friendliness provide much-needed comfort for the disturbed Shinji. However, suspicions abound over Kaworu's incredible synchronization abilities.

Instrumentality continues. The focus is primarily on Shinji now, as he learns to accept the individual’s ability to shape their world, and how the self cannot exist without others to define it.