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.

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...

Kouzou Fuyutsuki is kidnapped and interrogated by Seele, who are horrified over the results of the last encounter with an Angel. He recounts his past, providing flashbacks into the creation of Nerv. The pasts of Misato Katsuragi, Ritsuko Akagi, Rei Ayanami and Yui Ikari are also revealed. Ryouji Kaji, meanwhile, decides to find out the truth, no matter the cost.

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.

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 has begun, and now its inner process, the joining of all souls into one, will be depicted. The episode is primarily driven by dialogue, the background usually complete darkness. White text often appears on a black screen, an omniscient voice questioning the characters.

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.