Shinji Ikari is left emotionally comatose after the death of a dear friend. With his son mentally unable to pilot the humanoid robot Evangelion Unit-01, Gendou Ikari's NERV races against the shadow organization SEELE to see who can enact their ultimate plan first. SEELE desires to create a godlike being by fusing their own souls into an Evangelion unit, while Gendou wishes to revert all of humanity into one primordial being so that he can be reunited with Yui, his deceased wife.

SEELE unleashes its military forces in a lethal invasion of NERV headquarters. As SEELE's forces cut down NERV's scientists and security personnel, Asuka Langley Souryuu pilots Evangelion Unit-02 in a desperate last stand against SEELE's heaviest weaponry.

The battle rages on, and a depressed Shinji hides deep within NERV's headquarters. With the fate of the world resting in Shinji's hands, Captain Misato Katsuragi hunts for the teenage boy as society crumbles around them.

Shinseiki Evangelion Movie: Air/Magokoro wo, Kimi ni is an alternate version of the series ending, which either supplements or replaces episodes 25 and 26, depending on how they are viewed.

The movie was awarded the Animage Anime Grand Prix prize for 1997, the Japan Academy Prize for Biggest Public Sensation of the Year, and Special Audience Choice Award by the 1997 Animation Kobe.