| Summary
| - With the arrival of Evangelion Unit-03 in Tokyo-3, Toji Suzuhara is identified as the Fourth Child; Nerv offers better medical care for his sister if he agrees to become a pilot. While he agrees to the offer, Toji reveals to Shinji his fear of becoming an Evangelion pilot and apologizes for their initial encounter, finally understanding what Shinji must feel. While Shinji reassures Toji and accepts his apology, the subsequent activation test for Unit-03 goes horribly awry when the angel Bardiel infects it. When Rei and Asuka are defeated by angel, Gendo activates the dummy plug system in Unit-01 after Shinji, fearing for Toji's safety, refuses to attack Unit-03. Unit-01 brutally destroys the angel-infected Unit-03, but kills Toji in the process.
- 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.
- Asuka starts living in Misato's house and adapts to live in Japan, while she becomes friendly with Rei and Shinji. Meanwhile, Shinji goes with his father to visit his mother's grave, and tries to know him better. Ryoji Kaji, Misato's ex-boyfriend, is revealed to be a spy who investigates Gendo's job. He reveals to Misato and Shinji that the Angel, Adam, which caused the 2nd Impact that destroyed half of the human race, remains crucified in Nerv's headquarters. Kaji then explains to Shinji that the Evangelions are clones from Adam, and that Shinji's mother, Yui Ikari, was the one who created them. However, Yui was killed in a test subject from Unit-01, but her soul remains now in the Evangelion.
- Asuka Langley Soryu, another pilot from Evangelion, comes to Tokyo-3 to join to Nerv. Meanwhile, the Angel Israfel attacks the city, and Shinji and Asuka are sent to stop it. As it splits into two twins, the Angel easily defeats Shinji and Asuka, as none of them are able to cooperate. Nerv manages to damage the Angel, but it survives, being able to recover in a few days. Determining that it will be impossible to fight the Angel, Misato puts Asuka and Shinji in a training regimen which has them spending as much time together as possible in order to synchronize their biorhythms. By the end of the six days, Asuka and Shinji pull off the routine flawlessly, destroying the Angel.
- After Toji's death, Shinji vows never to pilot an Evangelion again, leaving NERV. As Shinji leaves, a new Angel attacks the city, but Units-00 and 02 are damaged, while Unit-01 rejects all the pilots NERV gives it. Before leaving the city, Kaji convinces Shinji to return to NERV to compensate Toji's death. Shinji goes to fight the Angel with Unit-01, but he is easily overpowered. In the fight, Unit-01's armor is broken, giving the Evangelion its own life, as the armor was only meant to maintain Unit-01 dead. Unit-01 then attacks the Angel, and ends eating it. As Unit-01 goes berserk, NERV freezes it, but they discover that Shinji has been ingested by Unit-01.
- Volume 6, interspersed through the events portrayed in volume 4, is separated into four different endings each focused on a pair of characters: the first story details Misato and Kaji deciding to continue their long distance relationship, the second story dealing with Ritsuko and Rei dealing with their unrequited loves , the third story is Touji's disappointment at not being able to pilot an EVA and his reunion with Hikari, and the final chapter has Shinji and Asuka getting into a fight and then subsequently understanding what they mean to each other.
- 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 Angel ended, but Seele invades Nerv to kill Gendo.
- To prevent the angel controlled Unit-00 from attacking, Rei self-destructs her Evangelion, destroying Tokyo-3. A few days later a relatively uninjured Rei is revealed, but has no memories of previous events and calls herself "The Third". Doctor Ritsuko Akagi reveals that Rei that was born from the Evangelion that killed Yui. It is revealed that Ritsuko's mother, Naoko Akagi killed the first Rei, since she was an abomination created by Gendo as a replacement for Yui. As such, the second Rei was the one that met Shinji, but apparently died when Unit-00 exploded.
- Shinji starts going to the school, but he eventually is attacked by his classmate, Toji Suzuhara, whose sister was injured during the time that Shinji used the Evangelion. Shinji is then summoned by Nerv to fight an attacking Angel, and his classmates Toji and Kensuke Aida follow him. In the battle, Shinji is pushed to his mental limit during the battle, going berserk during the last seconds. The Angel is defeated, but Shinji remains shocked. Misato questions Shinji's motivation to be an EVA pilot and sends him back to live with his uncle. However Misato realizes how Shinji was suffering with his uncle, and convinces Shinji to stay with her.
- The students learn they are being groomed to pilot Evangelions . Shinji and Rei are deployed to stop an Angel attack where, although he is initially paralysed with fear, Shinji manages to gather his nerves to save Rei and destroy the Angel.
- With the arrival of Evangelion Unit-03 in Tokyo-3, Toji Suzuhara is identified as the Fourth Child; NERV offers better medical care for his sister if he agrees to become a pilot. While he agrees to the offer, Toji reveals to Shinji his fear of becoming an Evangelion pilot and apologizes for their initial encounter, finally understanding what Shinji must feel. While Shinji reassures Toji and accepts his apology, the subsequent activation test for Unit-03 goes horribly awry when the angel Bardiel infects it. When Rei and Asuka are defeated by angel, Gendo activates the dummy plug system in Unit-01 after Shinji, fearing for Toji's safety, refuses to attack Unit-03. Unit-01 brutally destroys the angel-infected Unit-03, but kills Toji in the process.
- A new transfer student, Rei, starts at the school. Rei takes a liking to Shinji and confides her feelings to Asuka.
- A teenager named Shinji Ikari goes to Tokyo-3 city due to a request from his father, Gendo Ikari. While meeting with Misato Katsuragi, an employer from Gendo, the city is attacked by a giant created known as Angel, that confronts the army. Misato takes Shinji to NERV, an organization headed by Gendo that developed giant bio-mechanical mecha known as Evangelions. As the Evangelion Unit-01's pilot, Rei Ayanami, is injured, Gendo asks his son to pilot Unit-01 to defeat the attacking Angel. Shinji decides to fight the Angel, but he panics when seeing the Angel. Before being killed by the Angel, Shinji makes Unit-01 furiously attack the Angel, which self-destructs, causing minor damage to the Evangelion. Next day, while Shinji is recovering in the hospital, Misato discovers that Gendo is not planning to live with him. As such, Misato decides to be Shinji's legal guardian, to avoid him being alone.
- A teenager named Shinji Ikari goes to Tokyo-3 city due to a request from his father, Gendo Ikari. While meeting with Misato Katsuragi, an employer from Gendo, the city is attacked by a giant created known as Angel, that confronts the army. Misato takes Shinji to Nerv, an organization headed by Gendo that developed giant bio-mechanical mecha known as Evangelions. As the Evangelion Unit-01's pilot, Rei Ayanami, is injured, Gendo asks his son to pilot Unit-01 to defeat the attacking Angel. Shinji decides to fight the Angel, but he panics when seeing the Angel. Before being killed by the Angel, Shinji makes Unit-01 furiously attack the Angel, which self-destructs, causing minor damage to the Evangelion. Next day, while Shinji is recovering in the hospital, Misato discovers that Gendo is not planning to live with him. As such, Misato decides to be Shinji's legal guardian, to avoid him being alone.
- 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 Angel ended, but SEELE invades NERV to kill Gendo.
- Shinji starts going to the school, but he eventually is attacked by his classmate, Toji Suzuhara, whose sister was injured during the time that Shinji used the Evangelion. Shinji is then summoned by NERV to fight an attacking Angel, and his classmates Toji and Kensuke Aida follow him. In the battle, Shinji is pushed to his mental limit during the battle, going berserk during the last seconds. The Angel is defeated, but Shinji remains shocked. Misato questions Shinji's motivation to be an EVA pilot and sends him back to live with his uncle. However Misato realizes how Shinji was suffering with his uncle, and convinces Shinji to stay with her.
- Gendo Ikari reveals his true intent is to bring back whatever version of Yui he can. Rei refuses to become the spare and so Gendo shoots her, saying as he does that he can now use Shinji as an alternative. Kaworu tells the other characters of his angel status, but falls victim to Nerves new "anti angel" weapon. However he manages to recover sufficiently to rescue Shinji from Gendo's plan. In the coma induced scene witnessed by Shinji next Kaworu states that it was Shinji who made him "not want to destroy mankind." The Manga ends with Rei, Asuka and Shinji returning to school.
- While Shinji returns to Misato's house, he becomes friends with Toji and Kensuke. In Nerv, Shinji discovers that his father has a good relationship with Rei in contrast to the fact his relation with his son. Shinji tries to meet Rei, but she rarely responds to him. A new Angel, which takes the form of a floating monolithic metal diamond, appears in Tokyo-3 and nearly kills Shinji. As such, Misato devises a plan in which Unit 01 will use an advanced prototype positron rifle, which will use the entire electrical output of Japan in order to operate, while Rei uses Evangelion Unit 00 to shield Unit 01. The plan is successful with the Angel's death, and Rei smiles for the first time to Shinji.
- After Toji's death, Shinji vows never to pilot an Evangelion again, leaving Nerv. As Shinji leaves, a new Angel attacks the city, but Units-00 and 02 are damaged, while Unit-01 rejects all the pilots Nerv gives it. Before leaving the city, Kaji convinces Shinji to return to Nerv to compensate Toji's death. Shinji goes to fight the Angel with Unit-01, but he is easily overpowered. In the fight, Unit-01's armor is broken, giving the Evangelion its own life, as the armor was only meant to maintain Unit-01 dead. Unit-01 then attacks the Angel, and ends eating it. As Unit-01 goes berserk, Nerv freezes it, but they discover that Shinji has been ingested by Unit-01.
- Asuka starts living in Misato's house and adapts to live in Japan, while she becomes friendly with Rei and Shinji. Meanwhile, Shinji goes with his father to visit his mother's grave, and tries to know him better. Ryoji Kaji, Misato's ex-boyfriend, is revealed to be a spy who investigates Gendo's job. He reveals to Misato and Shinji that the Angel, Adam, which caused the 2nd Impact that destroyed half of the human race, remains crucified in NERV's headquarters. Kaji then explains to Shinji that the Evangelions are clones from Adam, and that Shinji's mother, Yui Ikari, was the one who created them. However, Yui was killed in a test subject from Unit-01, but her soul remains now in the Evangelion.
- Kaworu Nagisa is introduced as a new Evangelion pilot, but Shinji immediately hates him after Kaworu kills a stray kitten. Meanwhile, Asuka has problems synching with Unit-02 after suffering continuous defeat against the Angels; her fragile confidence is shaken when she must fight an Angel alone when Unit-02 is the only Evangelion ready for battle. However, the Angel invades Asuka's mind and makes remembers her past until she collapses from trauma, leaving Rei to throw the Lance of Longinus into space to destroy the Angel. With Asuka left comatose, Kaworu is assigned to be the pilot of Unit-02. Soon afterward, another Angel attacks Tokyo-3, but Shinji, Rei, and Kaworu's efforts are fruitless and Unit-00 is infected by the attacking Angel.
- The series climaxes with an assault on Tokyo-3 by multiple Angels, in which Shinji is ultimately brought into a form of Instrumentality, where he finally admits his feelings for Asuka. Afterwards, the pilots are split up to various training facilities across the world, with the story concluding several years later with them reuniting and unearthing a time capsule they buried together.
- Gendo's life as a troubled junior high student frequently involved in fights is chronicled. His relationship with a young Yui, his meetings with the enigmatic Kaworu, and how their lives change is detailed.
- Asuka Langley Soryu, another pilot from Evangelion, comes to Tokyo-3 to join to NERV. Meanwhile, the Angel Israfel attacks the city, and Shinji and Asuka are sent to stop it. As it splits into two twins, the Angel easily defeats Shinji and Asuka, as none of them are able to cooperate. NERV manages to damage the Angel, but it survives, being able to recover in a few days. Determining that it will be impossible to fight the Angel, Misato puts Asuka and Shinji in a training regimen which has them spending as much time together as possible in order to synchronize their biorhythms. By the end of the six days, Asuka and Shinji pull off the routine flawlessly, destroying the Angel.
- Kaworu invites Shinji to play at a concert with him. However, Shinji decides to take care of a sick Asuka. Kensuke is able to confess his feelings to Asuka and Rei is able to tell Shinji that she likes him.
- 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.
- 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 JSSDF's Evas, he awakens once again all of Unit-01's potential but the lost Lance of Longinus automatically stops the Eva which ends cruxified. Gendo then proceeds to initiate a Third Impact by merging with the second 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.
- While Shinji returns to Misato's house, he becomes friends with Toji and Kensuke. In NERV, Shinji discovers that his father has a good relationship with Rei in contrast to the fact his relation with his son. Shinji tries to meet Rei, but she rarely responds to him. A new Angel, which takes the form of a floating monolithic metal diamond, appears in Tokyo-3 and nearly kills Shinji. As such, Misato devises a plan in which Unit-01 will use an advanced prototype positron rifle, which will use the entire electrical output of Japan in order to operate, while Rei uses Evangelion Unit-00 to shield Unit-01. The plan is successful with the Angel's death, and Rei smiles for the first time to Shinji.
- Introducing Shinji Ikari as a school boy at NERV Catholic School along with Asuka and Rei. After seeing Rei with a mysterious boy in an alley way one night -who later turns out to be Kaworu- Shinji is exposed to the realities about the angels, receives his EVE, and joins the group of teenage children in their mission to fight them.
- SEELE sends JSSDF soldiers to kill the personnel from NERV. A mentally weakened Asuka is placed inside Unit-02 to fight against JSSDF's air forces. Having obtained supernatural powers from Adam, Gendo saves Shinji from the enemy and Shinji is taken by Misato to Unit-01 and assist Asuka. During the fight, Asuka recovers when realizing that her mother's soul is within the Eva and stops all JSSDF's forces. However, JSSDF sends Mass Produced Evas that overwhelm her. Meanwhile, Misato reaches the Eva's bay doors and sends him Shinji to it before dying while fighting the JSSDF soldiers. Having been requested by Misato to protect Asuka, Shinji prepares to use Unit-01 once again.
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