Unit-01 tries to make Shinji stay with him, but Rei communicates with the Eva to urge it to let him go. Shinji suddenly has a dream in which his mother convinces him to live. As such, Shinji's physical body appears outside Unit-01, having been inside it for a month. Meanwhile, NERV Subcommander Kōzō Fuyutsuki is kidnapped by SEELE, the organization that created NERV. SEELE members ask Fuyutsuki what Gendo has been doing in NERV, starting a series of flashback explaining how Fuyutsuki met Yui and Gendo. After the flashback, Kaji rescues Fuyutsuki, but he is soon killed by an unknown person due to his work as spy.
Stage 49: ...KissEdit
Shinji is inside Unit-01's Entry Plug after being ingested by it, and is now in a state of unseen being, and he saw the young him crying and asking his father not to leave him, who told that his mother is dead, and tells him to look behind him to see for himself. He saw the unarmored Unit-01, and Gendo orders Shinji to pilot it, he refused but saw himself watching Unit-01 choking Unit-03 and Toji dead. He then says to Gendo that he cannot leave with knife in his hand, and imagined that he killed his father. The Plug-Salvage Equipment has been installed on Unit-01, and Asuka is wondering about how Shinji will be, and Kaji tells her that everyone is worried about him, and leaves. Ritsuko talks with Maya about the plan and that when they used it ten years ago to "salvage" Yui Ikari, they failed. Kaji goes to talk with Misato and she asks him about things being kept from her, like Adam, Instrumentality Project, etc. and he tries to calm her down by kissing her, he pushed him for that, but noticed that he gave her something on their anniversary through their kiss.
Stage 50: Into The Heart...Edit
Shinji is still trapped in Unit-01, and he wonders how long he will stay there, and sees his mother there, and she tells him that he doesn't have to return and he can stay with her forever. Meanwhile, Rei have finished with the Dummy Plug Plant, and asks Gendo if he is going to see Unit-01, but he says that there is no need for him. Rei goes to see Unit-01 while wondering about herself, and demands on Shinji to return.
The Plug Salvage plan has started, and Shinji argues with Misato, Ritsuko, Kaji, Gendo and Asuka who tells him to return, but he refuses because he needs to rest instead of fighting. The plan begins to go the wrong way and Entry Plug has ejected, with the LCL carrying his clothes. Rei mentally talks with Shinji, revealing that his mother is not herself, but the Eva trying to manipulate him to stay.
Stage 51: MotherEdit
Rei made a mental contact with the Angelic part of Unit-01, and asks her not to take Shinji from her. Shinji screams in horror after knowing that it is not his mother, and cries for her to help, when his mother's soul got out of the Eva's Angelic part and glows very bright. Meanwhile, Misato is holding Shinji's clothes and invokes the Eva to return him. Shinji wakes up at a shore and notices his parents discussing how he can live after such mass hell, and she said that he can find paradise anywhere if he wills to live. Yui looks at Shinji and motivates him to return, declaring that she will always look after him. Shinji was "reborn" from the Eva, and Rei feels happy and tired after this. Kaji looks at his NERV ID card and notices how much it resembles the color of blood.
Stage 52: FlashbackEdit
Fuyutsuki is confused about Gendo's behavior towards his son, as he didn't go to visit him. Shinji meets Rei in the hospital, and thanks her though he doesn't know why. Misato is surprised to the news that the Dept. Commander Fuyutsuki is kidnapped, and she was taken into custody because the suspicious person is Ryoji Kaji. Meanwhile, Fuyutsuki is interrogated by SEELE, about the incident of Unit-01 taking the S² Engine to itself, and that cannot be acceptable, and they orders him to tell them everything that he knows about Gendo, and call him "Professor Fuyutsuki", a title he has not heard for long time, bringing back his memories.
In 1999, Kyoto Uni. Fuyutsuki remembers his first meeting with Yui Ikari, and he asks her about what she thinks for the future, if she is going join the bio-tech or join him in his lab, but she decided to create a family. Fuyutsuki is told about Gendo Rokubungi and to post bail for him. Gendo told Fuyutsuki that Yui told him, but Fuyutsuki's first thoughts about him weren't that good. Yui goes with Fuyutsuki and he asks her why she has chosen him, to hear her saying that he is just a lonely preson, and she found him endearing. But all the people were talking about the same result: Gendo married Yui Ikari for two reasons: Access to her groundbreaking thoeries, and the organization supplying her work, which he knew that it holds the German name "SEELE", of the soul.
Stage 53: A Giant Made Of LightEdit
In 2000, above Mt. Albert Markham, Antarctica, where the Second Impact occured. In 2002, at Antarctica, where nothing was left it except for the ice mountains, and on the ship that carries Gendo and Fuyutsuki, Fuyutsuki asked Gendo how he survived although he was on the Katsuragi Expedition, Gendo replied that he left one day before the incident, and he tells Fuyutsuki that he changed his name to Ikari. Yui couldn't come because she has to take care of their son. Fuyutsuki then asks him about SEELE, and Gendo tells him to think about joining him.
The official UN report was publicized that the Second Impact was just a natural disaster: A meteor, so tiny that there had been no warning yet so fast that hit Earth like cosmic sniper's bullet. Fuyutsuki noticed two suspicious images: The first was the last thing recorded by the Expedition cameras, and the second about the report with Gendo and Keel in the background. In 2003, Hakone, Japan, UN Artificial Evolution Labratory: Fuyutsuki has met with Yui again, and then goes to talk with Gendo and tells him that he and SEELE knew that the Second Impact was going to happen, and threatened to publish the whole truth. Gendo asks Fuyutsuki to go with him to the GeoFront, where he saw Naoko Akagi, who works on creating the Magi. Gendo and Naoko showed Fuyutsuki the Prototype clone of the "Giant of Light" which they, Gehirn, called Adam, and they are working on "reviving" Adam by the name Eva, and Gendo offers to Fuyutsuki to work together to write the Human's "own prophecy".
Stage 54: The Birth Of NERVEdit
Misato is still held at custody and expresses her fear of darkness, and how she wanted Kaji to be with her. Meanwhile, Rei and Shinji were in a garden and she talked with him about her feelings when she touched his hands, and she was happy the last she did, and asks him to if she can hold them again.
Back to 2004: Hakone Underground Experimental Facility 2, Fuyutsuki notices the 3-year-old Shinji in the Contact Experiment of Yui and Unit-01, and she apologizes saying it was her idea to bring him, to show him the "bright future for humanity", and seconds later, Yui's body dissloved into LCL and her remains absorbed into Unit-01. After the incident, Gendo has changed and then planned for the Instrumentality Project after discussing it with SEELE. Gehirn has been succeeded by NERV -German for nerve- and all the emplyees went along, except for the Magi's inventor, Naoko Akagi. Soon, Kaji rescued Fuyutsuki and says that he did that to get closer to the truth.
Stage 55: MessageEdit
The story continues with Kaji bleeding and someone arrives where Kaji is, and then shoot him. Misato has been released but haven't got any information about Kaji, who has been bleeding profusely and imagines his friends around him, and thanks them for coming. Misato returns home and stayed absent-minded until noticing a recorded message on the phone from Kaji, and break in tears after hearing it. Asuka tried to talk with her but of no use. Next day, Shinji returns home and Asuka asks him about what happened to Kaji, although he told her that he doesn't know, but he knew that he would be dead at the moment. Hyuga talks with Misato about the information he got about the beginning of the mass production, and she feels that the Committee is rushing for their plans, and tells Hyuga to look for more information, and she decided to see what the "soul kiss" Kaji gave her contains.
Stage 56: Of JealousyEdit
Ritsuko is talking with her grandmother about their cat and that it died. She then saw a picture of her, her mother and Gendo. Rei waits for Ritsuko for to take the injection, and tells that she was surprised by her change after only have her eyes on Commander Ikari, and that she thought Rei was only like a doll, and how both he and his son are wrapped around her finger. She then losed control after Rei rebukes her and tries to strangle Rei. Realizing that she was acting like her mother before her, she stops herself from killing Rei, but warns Rei against telling anyone what happened. At Misato's apartment, Misato, Shinji and Asuka have dinner together for the first time after Shinji's salvation from Unit-01, but it seemed awkward and gloomy there, when a call comes to Asuka from someone says that she is her mother. Shinji realized that the caller is Asuka's stepmother, because he heard Asuka before when she was asleep that her mother died just like his. Asuka screams at Shinji and goes to her room and yearns for her mother.
- ↑ Yui was not mentioned in their conversation, but in other talks, a connotation is refering to her
- Shinji, while still inside Unit-01, imagines that he killed his father.
- Misato got Kaji's information from their kiss, not while they were having sex.
- Unit-01's Angelic being tries to manipulate Shinji to stay by taking the shape of his mother.
- Rei makes a mental contact with Unit-01's Angelic being which resulted in exposing its real form.
- Rei goes with Shinji to talk in garden facility inside the GeoFront, which didn't appear in anime.
- For some reason, the manga version uses Unit-00 as the Eva Yui performs her contact experiment with, not Unit-01. It is not explained why.
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