Evangelion, renowned as the brainchild of Hideki Anno, is arguably what he's best known for. Part of that renown comes from how many times he's tried to give it a "satisfactory" ending. The first time was for the original TV series, Neon Genesis Evangelion, despite production difficulties. Unfortunately, dissatisfied fans were very vocal about their dissatisfaction. So when Anno went back to give his magnum opus a "proper" ending, the1997 film End of Evangelion seethed with underlying cynicism. For a long while, that was the definitive ending. That is until Anno returned to Evangelion with The Rebuild of Evangelion film series.
The fourth and final film in the series, Thrice Upon A Time, starts with Shinji wallowing in self-pity after his father, Gendo, duped him into helping him further his own apocalyptic agenda. Then a self-actualized Rei clone tells him about the happiness she's found, and thanks him for having done something so simple as talk to her--right before her clone body self-destructs. But the words reach Shinji, and rather than let them break him, as he might have once done, understands that he's not as useless as he thought, and moreover, he has a responsibility to confront his father and stop him from destroying reality just so he can be reunited with his wife, Shinji's mother, Yui. Finally, calmly and maturely, Shinji Ikari gets into the robot.
Daddy Issues
Initially, he and Gendo duel in identical Eva Units in a unique fusion of magical realism with science fiction. Their battleground shifts between a soundstage--a callback to the original ending of the TV series--and other locations previously seen throughout the series: the theater of life itself, and the pieces of the world that shaped them both. It quickly becomes clear however that settling things through combat is futile, but, in a move that throws the normally self-possessed Gendo off balance, Shinji makes the leap to reach out to him with words.
They find themselves on a moving train, a place they have in common as places they both seemed to escape to quite often in their youths, headphones blocking out the world. Gendo becomes vulnerable in this literal common ground, and admits that it was Yui who broke through his own shell as a young man. He confesses to how much her death broke and disconnected him from Shinji, all the while nursing the festering fear that his son would hate him if he knew the real him. As he relates this story, Shinji's age shifts from adolescence to the small boy he was when his father left him behind, when he was the one running away. But this time, instead of walking away again, Gendo turns around, embraces his son, and tells him he's sorry. This was something that never came to fruition in previous incarnations of either character.
Then his father disappears, and Shinji, an adolescent again, confronts others in his life whom he's hurt, and or been hurt by, in a sequence that makes callbacks to previous Evangelion moments. On the same beach beneath the same red sky as in End of Evangelion, rather than choking her, Shinji acknowledges that he has outgrown his feelings for Asuka, same as her, and thanks her with a smile. He tells the "original" Rei that one of her clones found her own sense of self, so there's no reason she can't either, while footage from the original series flashes between them, like memories from an alternate reality.
Then, when he intends to sacrifice himself in order to save the world, the spirit of his mother and father both step in and surrender their spirits instead. Their sacrifice rewrites the world into a reality that doesn't need Evangelions to exist. It's a cathartic sequence of letting go, both in story context and on a meta level, and it serves as positive response to the apocalyptic "Komm süsser Tod" sequence from End of Evangelion. Then Mari Makinami Illustrious, another Eva pilot and a Rebuild original character, sweeps in and pulls him out of the collapsing unreality around him.
A New World
The world remade, Shinji finds himself waiting on a bench on an animated recreation of Anno's hometown train platform, where characters like Rei, Asuka, and Kaworu, are all glimpsed briefly and appear to be living very normal lives. Shinji himself is an adult, wearing an actual suit and everything, though he also once more has the explosive collar from the third film around his neck. Then Mari, also wearing a business suit, comes up behind him and flirts with him the way she has been throughout the entire film series. But this time, instead of letting his insecurities get the better of him, Shinji is actually able to flirt back. As if he's passed some kind of test, Mari takes the collar off him, tells him he sounds like a "real grownup", and offers him her hand. He enthusiastically accepts. The camera pulls out, and the film turns from animated to live-action, with a live-action Shinji and Mari running out of the station in an overhead shot of Anno's hometown, perhaps signifying that Shinji is at last mature enough to face the real world.
Thrice Upon a Time is a fusion of End of Evangelion's higher production values with the positive self-affirmation of the original series. Coping with adulthood, with loss, with being with people even though it's difficult, all these things are at the core of what Evangelion expresses in the same way thoughts and feelings pour from a therapy patient during a session. Emotions are not logical, but they do represent truths about human nature. The point, arguably, was to visualize these abstract concepts through animation and turn them into something more positive than the cynicism that End of Evangelion embodied. Perhaps too, with time to grow themselves, some of the audience that had initially rejected Anno's original ending might have come to better understand what he was trying to say. More importantly, it's the ending Anno seemingly finally reaches for himself.