14 years after third impact, Ikari Shinji awakens to a world he does not remember. He hasn't aged. Much of Earth is laid in ruins, Nerv has been dismantled, and people who he once protected have turned against him. Befriending the enigmatic Nagisa Kaworu, Shinji continues the fight against the angels and realizes the fighting is far from over, even when it could be against his former allies. The characters' struggles continue amidst the battles against the angels and each other, spiraling down to what could inevitably be the end of the world. The film was retitled "Evangelion: 3.33" for its DVD/Blu-ray release.

In the aftermath of the Fourth Impact, stranded without their Evangelions, Shinji, Asuka, and Rei search for refuge in the desolate red remains of Tokyo-3. But the danger to the world is far from over. A new impact is looming on the horizon—one that will prove to be the true end of Evangelion.