Kaworu tries to befriend Shinji, but he continues ignoring him. Kaworu goes to converse with the SEELE members, who order him to attack NERV, revealing that Kaworu is an Angel controlled by SEELE. Kaworu pilots Unit-02 without entering in it, and goes to find Adam, but discovers the Angel within NERV is Lilith, not Adam. Thinking that Kaworu could make a Third Impact by touching Adam, Misato sends Shinji in Unit-01 to kill Kaworu. He asks Shinji to kill him, so that SEELE will not control his life. Shinji does so, but he remains saddened, unwilling to do anything. With Kaworu's death, the attacks from Angels ended, but SEELE invades NERV to kill Gendo.
Stage 71: Adam's OffspringEdit
After learning the shocking truth, Misato began to realize some of NERV's and SEELE's dark secrets. Kaworu met the third Rei, and she says that "he feels the same as her", and asks him why. Kaworu give her a clue that the matter that comprises them is the same, but what makes them different is who they lived for, and reminds her of what she (Rei II) said before. Shinji knew that Kensuke, Hikari and all his classmates have left the city, and that he won't have anyone he can call a friend. Kaworu tries to make friends with Shinji but the latter refuses his request.
Gendo interrogates Ritsuko for destorying the Dummy System, who answers that she was nothing to him the start, and begins to cry. Gendo goes to Unit-01 (Yui), and says that his goal of rejoining with her will soon be realized, and then swallows the embryo Adam. Kaworu talks with SEELE monoliths and they talk about how Lilin were the false successors of the Earth, and that their plan is to make humanity reborn as the true successors, children of God. Keel told Kaworu that Adam's soul exists within him, but its body in now within Gendo's body, and orders him to go to Terminal Dogma.
Stage 72: The Last MessengerEdit
Misato spies on Kaworu but couldn't know what is doing. Hyuga gave her the information he found about Kaworu's amazing ability to set his synchro ratio as he wants, and he tells her that he found the place where Ritsuko is being held at. Misato went to ask Ritsuko about the true identity of Kaworu. Ritsuko says that in 2000, people tried to return Adam to its embryonic form before the awakening of its offspring, which resulted in the occurrence of the Second Impact. She also said that among the data of the Katsuragi Expedition, there were attempts to use human genes to withhold Adam's soul, which she speculated to be Kaworu himself.
Kaworu goes to Unit-02 and activate it from outside the Entry plug to go to Terminal Dogma. NERV discovers that but Asuka is still in the hospital and there was no Entry Plug, which confirmed Ritsuko's speculations. Misato orders Shinji to go after Kaworu and kill him. Although hesitated at first, Shinji goes to pursue him and catch up, but have to fight Unit-02. Shinji tells Kaworu to stop, while fighting with Unit-02, while Unit-01's Prog Knife broke Unit-02's, it was about it clash with Kaworu, but he revealed A.T. Field to protect himself.
Stage 73: Arrival At The BarrierEdit
Kaworu reveals his A.T. Field, which surprised Shinji and Kaworu told him that everyone has an A.T. Field, which is "the barrier of the heart", but denies that saying the only the Evangelions and Angels have A.T. Field. Unit-02 attacks Unit-01 with its Prog Knife, which Shinji replied the same. Misato reminds Hyuga if Unit-01's signal disappears, then NERV should be self-destructed, to avoid the occurrence of the Third Impact.
Kaworu sets his A.T. Field to block every contact from happening, while they reached Terminal Dogma. Shinji tries to follow Kaworu but Unit-02 catches Unit-01's leg, while Kaworu has reached the giant crucified being, which he identified as Lilith. Shinji defeats Unit-02 and goes to Kaworu, who tells what will happen when he make the Third Impact occurs, and that his life doesn't matter, and wishes Shinji to kill so he can be free. Shinji is confounded and tells Kaworu it isn't fair to die like this.
Stage 74: A Fistful Of MemoriesEdit
After a brief silence, a new A.T. Field was detected descending into Terminal Dogma, but soon it vanished. Meanwhile at Terminal Dogma, Shinji still won't accept Kaworu's request to kill him, which Kaworu said that Shinji must hate him very much. Shinji denies hating him and hesitates, but then begin to squeeze Kaworu inside Unit-01's palm. Soon after that, the monitors have recovered, revealing only Unit-01's signal. He imagines himself strangling Kaworu on the day they met, presumably after he kille the stray cat. Misato goes to Shinji who doesn't seem to look good, and tells him that they will stay at headquarters the nest day. Shinji while thinking about Misato's words, thinks that the things he wanted to protect are getting lost of him, and asks himself if this world really have to be protected.
Stage 75: The Missing HeartEdit
Shinji found out he was drawn to Kaworu without knowing that, even though he thought that he doesn't need friends anymore, and asks why do people become drawn to others more than themselves. Misato then tells him this happens because humans are imperfect beings who cannot live alone, but despite that, they have to go on living. Shinji became more devastated and tells about what he really was feeling and suffering, and she tries to slap, but stops herself and then he left the car to NERV.
NERV is still on "Level-1 Alert", even though the Angels' attacks stopped. SEELE discusses their current matters including Tabris' unsure betrayal for them, and then plan to to have Gendo killed for defying their schemes for his own. Gendo states to Fuyutsuki that even if Tabris had contacted Lilith, "...the Instrumentality Project would have ended incomplete, because the main essential factor on the Project "Lilith's broken... heart" was missing." with Rei being with them.
Shinji goes to visit the comatose Asuka after suffering from Kaworu's death. He then pleads to her, asking her to wake up and do what she used to do to him, and then says that "the Asuka I want to protect isn't an empty shell." These words woke Asuka up and she tries to strangle Shinji, but the doctors went to stop her and he was escorted out of her room. Shinji notices Rei walks with Gendo and she looked at him with indifference, and then left. This thing had signaled to Shinji the end of his life with others, as he lost his friends one after another, and breaks in tears outside Asuka's room.
Stage 76: The Final EnemyEdit
Misato hacks into SEELE's systems and explores the true meaning of having thirteen Evangelions, and the plan behind the Human Instrumentality Project "to unite the separated and imperfect humans into perfect single entity, but this time not using NERV, but the Evas. SEELE invasion on NERV has begun by hacking through the Magi system by five Magis, three of them are from China, Germany, and the USA. Misato calls Hyuga about the current status, which he answered that the Tokyo-2 has issued an executive order A-801, which the abolishment of special legal protection on NERV and transfer all command to the Japanese government. Maya call Misato and tells her that Dr. Ritsuko Akagi is now making a counter-measures to the hacking on Magi. Ritsuko is working on creating a defensive firewall against the hacking, even though she said that what she does now is foolish. The firewall has been installed and became protect for sometime, and Ritsuko says "see you again, mother." SEELE, after knowing of NERV's installation of a type-666 firewall, orders the JSSDF to invade NERV.
SEELE's goal is to take over NERV as a base along with the two Eva Units (and the elimination of Gendo). NERV assumes Level-1 battle stations, as in an Angel attack. Shinji hears the Level-1 battle stations call, and he knows he should get to Unit-01, But he cannot move. The Special Forces are ordered to kill the Eva pilots, and Shinji is left completely vulnerable to their attack as he sits unattended and unmonitored in NERV’s break room, unable to move.
- Rei went to Terminal Dogma later than the anime, and thus didn't help Shinji in stopping Unit-02.
- When Shinji visited Asuka in The End of Evangelion, Asuka didn't wake up and then he masturbated next to her bed, but in the manga she wakes up and strangled him.
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