In 2015, fifteen years after a global cataclysm known as the Second Impact, the child Shinji Ikari is summoned to Tokyo-3 by his estranged father Gendo, the commander of the paramilitary organization NERV. Shinji is caught in the crossfire between UN forces and an angel, an alien lifeform; colonel Misato Katsuragi rescues him and brings him to NERV headquarters. Gendo demands Shinji pilot Evangelion Unit 01, a giant bio-machine, against the angel. Shinji concedes when Gendo threatens to send Rei Ayanami, a wounded Evangelion pilot, into battle instead. Shinji wins the fight after Unit 01 goes berserk and destroys the Angel.
Misato becomes Shinji’s guardian and he is enrolled in the local middle school. When another angel arrives, Shinji’s classmates Toji Suzuhara and Kensuke Aida sneak out of the emergency shelters to watch the battle. The angel slams Unit 01 into a mountainside, nearly crushing Toji and Kensuke. Misato has the two take cover in Unit 01’s cockpit and orders Shinji to retreat, but he ignores it and destroys the angel with Unit 01’s knife.
The Sixth Angel appears and begins drilling into Tokyo-3 to reach NERV headquarters. When Shinji attacks it in Unit 01, the Angel fires a powerful laser, critically injuring him. He wakes from a coma some time later and Rei tells him she will take his place and leaves for the mission alone.
To motivate the despondent Shinji, Misato takes him to the deepest level of NERV headquarters and shows him a giant white being crucified to a cross-like restraint: the Second Angel, Lilith. Misato explains that the angels are attempting to initiate contact with Lilith and bring about Third Impact and the end of all life on Earth.
Shinji agrees to pilot Unit 01 against the angel alongside Rei in Unit 00. He destroys it with an experimental positron rifle, which requires the entire electrical power output of Japan to power. 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, Kaworu Nagisa awakens from one of nine coffin-like containers arranged on the surface. In a pit in front of him, surrounded by construction equipment and scaffolds, 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 at all and that he looks forward to meeting Shinji.