The Ending Of End Of Evangelion Explained

In the world of Neon Genesis Evangelion, humans are descendants of an uber-being called Lilith. Both the original series finale and the film revolve around an apocalyptic event called Human Instrumentality, which merges all humans with Lilith into a single consciousness. Different factions in Evangelion want to bring about Human Instrumentality for different reasons throughout the series. In short, in both the series finale and End of Evangelion, Human Instrumentality begins, and at its center is protagonist Shinji Ikari.

The End of Evangelion offers a sort of revised, definitive version of the final two controversial episodes of Neon Genesis Evangelion. That said, the final moments of the series and its companion film are diametrically opposed. In Neon Genesis Evangelion, Shinji seemingly accepts Human Instrumentality. In its iconic final moments, the depressed and rudderless Shinji claims agency over his life for the first time. He then receives congratulations from the series' key characters, with whom his consciousness has merged. 

In The End of Evangelion, Shinji rejects Instrumentality, and finds himself stranded on a desolate, post-apocalyptic Earth with only Asuka by his side. The ending of the series is hopeful in tone but bleak in implication, given that Shinji's newfound bliss appears to be a product of Instrumentality rather than his own free will. The End of Evangelion, then, presents a more hopeful future for Shinji, despite the literal destruction of nearly everything around him.