Shinji pilots Unit-01 and saves Asuka from the mass produced Evas. Meanwhile, Ritsuko tries to self-destruct the NERV facility to stop Gendo's plan but she fails and is shot by Gendo. While Shinji is dealing with SEELE's Evas, he awakens once again all of Unit-01's potential but the lost Spear of Longinus automatically stops the Eva which ends cruxified. Gendo then proceeds to initiate a Third Impact by merging with the third Rei who possesses the DNA from Lilith. However, Rei rejects Gendo and combines with Lilith, becoming a growing being that holds Unit-01 and confronts Shinji's mind.
Stage 84: CallingEdit
Unit-01, piloted by Shinji, reaches the GeoFront as Asuka in Unit-02 is still fighting the Mass Production Evangelions, saving her from an imminent death. Shinji then charges at the MP Evas with one of their spears. Meanwhile, in Terminal Dogma, Gendo with Rei reach Lilith in order to start Gendo's desired version of Third Impact by the fusion between Adam and Lilith. However, Ritsuko appears to them, intending to prevent Gendo from initiating his plan.
Stage 85: BetrayalEdit
Shinji has manages to incapitate all the MP Evangelions, but they reactivate due to the S² Engine equipped within them. In Terminal Dogma, Ritsuko threatens to activate a self-destruct mechanism she installed into the Magi along with the protective firewall, which would destroy NERV Headquarters. However, Casper denies her access, allowing Gendo to shoot and kill her. Back to the GeoFront, the MP Evangelions begin attacking Units 01 and 02.
Stage 86: The Ceremony BeginsEdit
Shinji asks his mother to give him strength, increasing Unit-01's sychro ratio to 250%, revealing the Eva's hidden potential. This stimulates the lost Spear of Longinus and causes it to return to Earth, stopping Unit-01. The MP Evangelions began crucifying Unit-01 with their own spears. Unit-01 is detained by SEELE, and Fuyutsuki assumes that SEELE is planning to use Unit-01 as a Medium.
Stage 87: RejectionEdit
Gendo begins his plan for the Third Impact by the fusion between Adam, which he has in his palm, and Lilith, whose soul is within Rei's body. Meanwhile, while Unit-01 has been crucified, SEELE members says that "Unit-01 has been marked with the Stigma", and the MP Evangelions began resonating their S² Engine to start the Human Instrumentality Project. Back in Terminal Dogma, Rei rejects Gendo and absorbs Adam from Gendo's hand, and then goes saying that "Ikari is waiting" despite Gendo's begging from her.
Stage 88: Black MoonEdit
The Sephirot has been formed by the MP Evangelions as a part of SEELE's plan, and very strong explosion appears on the surface, destroying all of the JSSDF troops. The GeoFront begins to shatter revealing its true form, the Black Moon. Rei, who has absorbed Adam, has fused with Lilith and is heading outside of Terminal Dogma. As Gendo still begging Rei to come back, Ritsuko shoots him with a pistol in his throat, as she denies his words earlier about his love to her, and falls again.
Stage 89: Face to FaceEdit
Unit-01 is still restrained while Shinji wonders what will happen to everyone. As a giant white figure of Rei appears before him, Shinji screams horrified and the MP Evangelions begin sychronizing with Rei and amplifiying their A.T. Fields to assimilte with her. Shinji's ego becomes weaker, and Keel proclaims that "the time for third retribution is now."
The Spear of Longinus fuses with Unit-01, forming the Tree of Life. Rei confronts Shinji's mind and asks him about his wish. The Black Moon continues to ascend as Lilith/Rei begins generating an Anti A.T. Field, as the chamber of Guf, the chamber of souls, opens. Lilith spread its Wings of Light, beginning the Third Impact.
Stage 90: Memories of SummerEdit
Rei asks Shinji about what his wishes and thoughts and "his everying". He now begins to remember his past when his mother is still alive, and the weather is so hot, and Yui tells her son about seasons before and that she will show him the snow someday. Shinji's memories go to when his father left him under his uncle's care. Shinji's cousin tells him about what happened to his mother, and Shinji is angered by that and fights with him, Shinji then apologizes and promises not to fight anymore and asks his uncle's family not to talk bad about his parents.
Shinji is in school and doesn't seem to be liked by his classmates, and he is also the only one who didn't finish his schoolwork. He then remembers when he went with his father to his mother's grave. Shinji then says that he cannot remember something important that his mother told him before she disappeared.
- A premium edition of this chapter was released in Japan.
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