In 2015, fifteen years after a global cataclysm known as the Second Impact, fourteen-year-old Shinji Ikari is summoned to Tokyo-3 by his estranged father Gendo, the commander of the paramilitary organization Nerv. Shinji gets caught in the crossfire between UN forces and a mysterious being called an Angel, but is rescued by Captain Misato Katsuragi, who brings him to Nerv headquarters. There, Gendo demands Shinji to pilot Evangelion Unit 01, a giant, humanoid bio-machine, against the Angel. Shinji concedes when Gendo has Rei Ayanami, a wounded Evangelion pilot, prepared to be sent out instead. Shinji loses consciousness during the fight due to injuries inflicted by the Angel on Unit 01, as Evangelion units sympathetically reflect the pain of injuries they sustain onto their pilots. Unit 01 autonomously reactivates and wins the fight, destroying the Angel. After the battle, Misato becomes Shinji's guardian and he is enrolled in a local junior high school. When another Angel arrives, Shinji's classmates Toji Suzuhara and Kensuke Aida sneak out of their emergency shelter to watch the battle, but the Angel throws Unit 01 onto a mountainside, nearly crushing them. Misato has the two take cover in Unit 01's cockpit and orders Shinji to retreat, but he ignores the orders and destroys the enemy with Unit 01's knife. After Misato scolds him for insubordination, Shinji wanders off and is recovered by Nerv agents before being brought back to her.
The Sixth Angel appears, but when Shinji is sent out to attack it in Unit 01, the Angel fires a powerful laser, critically injuring him, before beginning to drill into Tokyo-3 to reach Nerv headquarters. He wakes up from a coma several hours later, and Rei tells him that she will take his place for the operation to stop the Angel, and leaves to do it alone. Misato shows Shinji what the Angels are trying to reach: a white anthropomorphic giant kept at the bottom of Nerv headquarters, the Second Angel, Lilith, which upon contact with one of the attacking Angels will result in the deaths of all of the life on Earth. Shinji agrees to pilot Unit 01 alongside Rei in Unit 00, wielding an experimental positron cannon, which requires the entire electrical power output of Japan to power, like a sniper rifle, and successfully destroys the Angel. Rei is nearly killed defending Shinji from the Angel's return fire, but he saves her by cooling Unit 00 in water and prying open its cockpit using Unit 01's knife. Rei, normally cold and emotionless, shares a smile with him.
On the surface of the Moon, a boy named Kaworu Nagisa awakens from one of nine coffin-like containers arranged on the ground. In a pit in front of him, surrounded by construction equipment and scaffolding, is an unidentified giant wearing a purple seven-eyed mask and wrapped in white bandages. A black monolith appears through which he and Seele 01 engage in a cryptic conversation. Looking towards Earth, Kaworu says that "the third one" has not changed and that he looks forward to meeting Shinji.
