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...

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.