In 2015, fifteen years after a global cataclysm known as the Second Impact, teenagerShinji Ikariis summoned to the futuristic city of Tokyo-3 by his estranged fatherGendo Ikari, director of the special paramilitary force Nerv. Shinji witnessesUnited Nationsforces battling an Angel, one of a race of giant monstrous beings whose awakening was foretold by theDead Sea Scrolls. Because of the Angels' near-impenetrable force-fields, Nerv's giant Evangelion bio-machines, synchronized to the nervous systems of their pilots and possessing their own force-fields, are the only weapons capable of keeping the Angels from annihilating humanity. Nerv officerMisato Katsuragiescorts Shinji into the Nerv complex beneath the city, where his father pressures him into piloting the Evangelion Unit-01 against the Angel. Without training, Shinji is quickly overwhelmed in the battle, causing the Evangelion to go berserk and savagely kill the Angel on its own.
Following hospitalization, Shinji moves in with Misato and settles into life in Tokyo-3. In his second battle, Shinji destroys an Angel but runs away afterwards, distraught. Misato confronts Shinji and he decides to remain a pilot. The Nerv crew and Shinji must then battle and defeat the remaining 14 Angels in order to prevent the Third Impact, a global cataclysm that would destroy the world. Evangelion Unit-00 is repaired shortly afterwards. Shinji tries to befriend its pilot, the mysterious, socially isolated teenage girlRei Ayanami. With Rei's help, Shinji defeats another Angel. They are then joined by the pilot of Evangelion Unit-02, the multitalented, but insufferable teenagerAsuka Langley Sōryu, who is German-Japanese-American. Together, the three of them manage to defeat several Angels.
Shinji is forced to fight an infected Evangelion Unit-03, and watches its pilot, his friend and classmateToji Suzuhara, incapacitated and presumably permanently crippled (killed in the manga). Asuka loses her self-confidence following a defeat, and spirals into depression. This is worsened by her next fight, against anAngelwhich attacks her mind and forces her to relive her worst fears and hidden insecurities, resulting in a mental breakdown. In the next battle, Rei self-destructs Unit-00 and dies to save Shinji's life. Misato and Shinji visit the hospital where they find Rei alive but claiming she is "the third Rei". Misato forces scientist Ritsuko Akagi to reveal the dark secrets of Nerv, the Evangelion boneyard and the dummy plug system which operates using clones of Rei. These succession of events leave Shinji emotionally scarred and alienated from the rest of the characters.Kaworu Nagisareplaces the catatonic Asuka as pilot of Unit-02. Kaworu, who initially befriends Shinji and gains his trust and affection, is in truth the final foretold Angel, Tabris. Kaworu fights Shinji, then realizes that he must die if humanity is to thrive and asks Shinji to kill him. Shinji hesitates but eventually kills him. He is overcome with guilt.
After the final Angel is defeated, Seele, the mysterious cabal overseeing the events of the series, triggers the "Human Instrumentality Project", a forced evolution of humanity in which the souls of all mankind are merged for benevolent purposes, believing that if unified, humanity could finally overcome the loneliness and alienation that has eternally plagued mankind. Shinji's soul grapples with the reason for his existence and reaches an epiphany that he needs others to thrive, enabling him to destroy the wall of negative emotions that torment him and reunite with the others, who congratulate him.