Teenager Shinji Ikari is the pilot of Evangelion Unit 01, one of several giant cyborgs designed to fight hostile supernatural entities called Angels. Distraught over the death of Kaworu Nagisa, Shinji visits fellow pilot Asuka Langley Soryu in a hospital and masturbates to her unconscious body, but regrets it immediately afterwards.
The shadowy committee SEELE discovers that Gendo Ikari intends to use NERV, the paramilitary organization that deploys the Evangelion units, for his own plans. SEELE dispatches the Japanese Strategic Self-Defense Force (JSSDF) to seize control of NERV, killing most of the staff. NERV major Misato Katsuragi orders Asuka moved to the cockpit of Evangelion Unit 02 and placed at the bottom of a lake, then rescues Shinji from JSSDF troops. Determined to have Shinji defend NERV, Misato brings him to Unit 01’s bay doors, but is shot in the process. Before her death, Misato implores Shinji to pilot Unit 01, kisses him, and forces him into the elevator. Shinji discovers Unit 01 immobilized in bakelite.
Concluding that NERV’s defeat is inevitable, Gendo retrieves Evangelion pilot Rei Ayanami. He plans to use her to initiate the Third Impact, a cataclysm which will kill everyone on Earth and reunite him with his deceased wife, Yui. Attempting to stop him, NERV scientist Ritsuko Akagi sends a computer command to destroy NERV. Casper, a computer core modeled on Ritsuko’s mother, overrides her command and Gendo kills her. Meanwhile, inside Unit 02, Asuka overcomes her trauma and re-activates the unit. She destroys the JSSDF forces, but SEELE unleashes a fleet of new mass-produced Evangelion units, who disembowel her and Unit 02. Unit 01 breaks free of the bakelite and ascends above NERV headquarters. From the cockpit, Shinji sees the mass-produced units carrying the mutilated remains of Unit 02 and screams in terror.
Gendo attempts to merge with Rei, who carries the soul of Lilith, an angel hidden beneath NERV headquarters, to begin Third Impact. Having merged with another angel, Adam, he will become a god if he merges with Lilith; however, Rei rejects Gendo, absorbs Adam, and reunites with Lilith, growing to a gargantuan size. The mass-produced Evangelion units pull Unit 01 into the sky and crucify it with the Lance of Longinus, which transforms into the “Tree of Life”, beginning the Third Impact.
After several dreamlike contemplations, including a fight with Asuka, Shinji decides that he is alone and everyone in the world should die. In response, Rei/Lilith dissolves humanity back into LCL, a conscious primordial soup, reforming the souls of humanity into a single consciousness. Shinji rejects this new state when he realizes that life is about experiencing joy as well as pain. Unit 01, seemingly moving on its own, breaks free of the Tree of Life, wielding the rematerialized Lance of Longinus to destroy the Mass Production Units and end Third Impact. Rei/Lilith’s body splits into pieces, crashing to the surface of the Earth.
Shinji awakens on a shoreline littered with the wreckage of Mass Production Units and the body of Rei/Lilith, and finds that Asuka has also rematerialized. He begins to strangle Asuka, but when she caresses his face, he stops and breaks down in tears.