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.
It seems like it's an important day for nearly everyone at NERV. Misato and Ritsuko are going to a wedding; Shinji and Gendo are visiting Yui's grave; Asuka has a date. However, important things will spring from these seemingly mundane events.
Shinji beats Asuka in a synch test, much to her annoyance. Not too long after, the EVAs are dispatched to deal with a mysterious apparition, and EVA-01 is sucked into a shadowlike blackness that materializes out of nothingness from under it. While an emergency operation to rescue the captured EVA is concocted, Shinji goes on a trip into the depths of his own consciousness...
A NERV branch in Nevada is obliterated in a catastrophic accident, and NERV headquarters prepares to station a new Evangelion in Japan. The Fourth Child is selected, unbeknownst to Shinji.
Evangelion Unit-03 arrives from the United States. However, its activation experiment brings out NERV's worst nightmare when it turns out to have been infected by the Thirteenth Angel. The other EVAs are dispatched to battle the Angel-infected abomination... even at the risk of killing its helpless pilot.
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...