"The End of Evangelion" completely reframes the ending of the original series by depicting the physical events of the Third Impact. The plot's major turn is the revelation that SEELE's true purpose was to intentionally initiate this apocalypse, using NERV and the Angels as pawns all along. They unleash the Japanese Strategic Self-Defense Force to massacre everyone at NERV HQ to gain control of the Evas.
A key twist occurs when Rei Ayanami, who was believed to be Gendo Ikari's loyal puppet, defies him at the crucial moment. Gendo intends to merge with the embryonic Adam and the soul of Lilith (within Rei) to orchestrate his own version of Instrumentality to reunite with his dead wife, Yui. Instead, Rei absorbs Adam and rejects Gendo, choosing to give control over humanity's fate to Shinji.
Asuka's character has a triumphant, yet ultimately tragic, final arc. She realizes her mother's soul was always protecting her from within Eva Unit-02, allowing her to overcome her trauma and fight magnificently. However, she is horrifically killed by the nine Mass Production Evas, which are revealed to be immortal and powered by dummy plugs based on Kaworu Nagisa. Her gruesome death is a catalyst for Shinji's final mental breakdown, which triggers the Third Impact.
The climax reveals the ultimate nature of the Human Instrumentality Project: the merging of all human souls into a single entity, dissolving all individuality. Shinji, at the center of this event, initially wishes for this world without pain where everyone can just die. However, through a series of surreal visions and dialogues, he realizes that a world without others is meaningless and that joy cannot exist without sadness. He rejects Instrumentality, allowing humans with a strong enough will to live to reform their bodies from the primordial Sea of LCL. The final, enigmatic scene shows Shinji and Asuka as the first (and perhaps only) two to return. Shinji's attempt to strangle Asuka, and her subsequent caress, symbolizes their deeply dysfunctional relationship and the painful, uncertain reality he has chosen over a painless void.