Misato brings Shinji, along with Touji and Kensuke, to a massive UN naval convoy transporting Evangelion Unit-02 and its fiery German pilot, Asuka Langley Souryuu, to Japan. Escorting Asuka is Misato's old boyfriend, Ryouji Kaji. After some awkward introductions and reunions, the fleet is attacked by a massive aquatic Angel. Asuka powers up Eva-02, and decides that she will defeat the Angel by playing "hopscotch"...

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.

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...

Shinji achieved an unprecedented 400% synchronization ratio with EVA-01 during the battle with Zeruel, to horrible effect. With the EVA having ascended to the status of a living God and Shinji absorbed inside it, Ritsuko unsuccessfully attempts to recover him.

Asuka's synch rate is on a downward spiral after her defeat at the hands of the Fourteenth Angel, Zeruel, and her frustration with Rei, Shinji, Misato and Ryouji is on the rise. Angrier and more disturbed than ever, she is forced to relive her dark, traumatic past during the encounter with the Fifteenth Angel, Arael.

Asuka sinks into deep depression after Arael's mental probing, and is unable to pilot when the new Angel Armisael arrives. Armisael begins physically fusing with EVA-00 and threatens to do the same to EVA-01, prompting Rei to sacrifice herself to save Shinji, only to appear alive soon afterwards.

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.