Neon Genesis Evangelion has a reputation for having one of the most confusing endings in all of anime, and anyone who’s watched it would surely agree. While the ending of the series may not be particularly clear to most viewers, it does have some real meaning behind it, and isn’t just weird for the sake of being weird. The anime’s ending is best understood with the context provided by the End of Evangelion movie, which should help to clarify some of the more confusing points.
Evangelion is pretty straightforward to follow right up to the last two episodes, where the show begins to break from traditional narrative style for a more experimental (and far less clear) style. In episode 25 of the series, the Human Instrumentality Project, which has been discussed heavily but not explained, is put into motion. The goal of Evangelion‘s Instrumentality was to dissolve the “AT Fields” that exist around a human soul, keeping it distinct from other souls. These are the same AT Fields which the EVA units used to protect themselves from Angels, further confirming the biological nature of EVAs.
When Instrumentality activates, the minds and souls of every human on Earth are joined together into one collective unconscious. The images and scenes shown in episodes 25 and 26 are set in this mental realm, not in reality, hence their confusing, dreamlike nature. Shinji, Rei, and other characters contemplate why they exist as separate beings, and if that’s worth all the suffering that it causes. In episode 26, Shinji sees an alternate version of his life without Evangelions–a peaceful world where he has friends and his family is happy.
This is just a fantasy, however, and Shinji can’t accept this fantasy world as real. It does, however, help him to realize that his life doesn’t have to be the way that it has been–it’s not necessary for him to suffer in misery and loneliness. There are other lives he could lead besides that of an EVA pilot. This gives Shinji the courage to accept himself and the world, prompting congratulations from the other characters, who are shown in a circle, applauding around him.
The movie The End of Evangelion presents an alternate perspective on the events of episodes 25 and 26, to the point where the movie is effectively broken into two parts: episode 25′ and episode 26′. These parts of the movie depict what was happening in the real world at the same time as the scenes within Instrumentality from the series, providing context to some glimpses of reality seen in the series proper.
Following the defeat of the final Angel, NERV and the secretive group SEELE immediately go to war, as Gendo has his own plans for Instrumentality which differ from SEELE’s. SEELE arranges for a massive attack on NERV HQ, first by the Japanese Self Defense Force and then by 9 mass production EVAs. While Asuka seemingly manages to defeat the EVAs, they slowly get back up right as Unit 02 is running out of battery power, destroying it and killing Asuka. Shinji finds Unit 02 destroyed and realizes that Asuka is gone.
Rei, meanwhile, has begun to merge with Lilith, the being kept underneath NERV HQ. Rei, as a clone, was designed to be a human vessel for Lilith, but she doesn’t give Gendo what he wants, instead allowing Shinji to shape the fate of humanity by deciding how Instrumentality will play out. Shinji’s hatred for the world as-is leads to the dissolution of all AT Fields, with people shown transforming into puddles of LCL–the same liquid which fills the inside of the EVAs. The merged Lilith takes on Rei’s appearance and personality, becoming the giant seen in the film.
Within the mental realm of Instrumentality, Shinji experiences many visions of the past, and speaks with other characters like Misato, Asuka, and Rei, who can no longer conceal anything from him. He begins to think it might be better if humanity was destroyed, and Lilith begins absorbing human souls. However, Instrumentality has done little to end the loneliness that Shinji felt, and he rejects it, causing AT Fields to begin recreating themselves, and allowing him to reform as an individual alongside Asuka. Shinji realizes that though connecting with people is difficult and scary, it may ultimately be worth it.
Rebuild of Evangelion takes place in a very different continuity, one which moves into the far future relative to the original series. Shinji and the other EVA pilots haven’t aged at all, however, as a consequence of becoming EVA pilots. At the beginning of the final movie, Shinji is almost fatally depressed after watching Kaworu’s death, and takes quite a long time to recover in a small village. There, he gets to know a new clone of Rei, who eventually dissolves into LCL, which finally forces him to attempt to face his trauma.
Gendo’s plan for Instrumentality is even more complicated here than it was in the series. He brings forth the “Black Moon,” a ship of some sort that brought Lilith to Earth, and which was buried under NERV HQ. With a Third Impact having already taken place before the time skip, Gendo intends to bring about a Fourth Impact to establish Instrumentality. He is able to turn the Black Moon into two new Spears of Longinus, and heads to the site of the Second Impact to bring it about himself.
Gendo explains that he has become beyond human, and that humanity was always destined to either destroy the Angels or be destroyed by them. He enters a mysterious portal with EVA Unit 13, and is followed not long after by Mari Makinami and Shinji in Unit 08. Shinji enters Unit 01 and achieves an infinite sync rate, allowing him to regenerate the EVA to its former glory. Shinji takes one of the Spears from Gendo and transforms it. In a realm where physical laws don’t apply, Gendo and Shinji battle it out for the fate of humanity.
Gendo takes the opportunity to show Shinji “Evangelion Imaginary,” a hypothetical EVA that can only exist here. Gendo intends to use the Evangelion Imaginary to rewrite reality and bring about Instrumentality that way. Shinji challenges his father’s beliefs and tries for the first time to understand him. Their problems of loneliness and isolation are fundamentally the same, and Shinji manages to get through to him. Gendo apologizes to Shinji and disappears. Still in the imaginary space, Shinji decides to keep the world as it is, but erase the existence of Evangelions.
The spirits of Gendo and Yui use Unit 13 to make Shinji’s wish a reality, and the film ends with adult versions of the EVA pilots (suggesting they were never pilots in this reality) at a train station, with Shinji seemingly in a relationship with Mari. It closes out with live-action shots of series creator Hideaki Anno’s hometown, which are very much open to interpretation.
While Evangelion was an original anime, it was adapted as a manga to promote the series, which ran from 1994 to 2013. Many of the events of the anime and manga are roughly similar, but the manga has a very different ending from any of the anime projects.
The manga adapts the events of End of Evangelion and the final episodes of the series, but takes them in a wildly different direction. As a result of differences in how the manga characters evolved compared to their anime counterparts, some decisions were made differently, radically affecting the end. Shinji, for example, gets into Unit 01 sooner and is able to save Asuka from dying to the Mass Production EVAs as she does in End of Evangelion.
The final volume of the manga sees giant Rei emerge, like in the film, and enact Shinji’s apparent wish for a world without separation… but Shinji suddenly objects. Shinji breaks contact with Rei, noting that this world of Instrumentality is no different than death. Rei explains that returning to being individual beings will mean the return of the pain of separation, but Shinji accepts that, noting that they can only have moments of joy the way things were.
The giant Rei begins to fall apart as instrumentality is undone, and the Mass Production EVAs are destroyed as well, falling down to Earth. Shinji says farewell to Rei, who thanks him for being a friend to her. Shinji then, from within Unit-01, sees a vision of an island rising from the water, where his mother, and later his father, are waiting. Yui promises to watch over Shinji always, and Shinji says goodbye to his parents for the last time.
The world is able to return to its previous state, but not the state it was in before Third Impact. Instead, the world takes on the state it had before Second Impact, undoing the damage that did and returning life on Earth to normal. No red seas or eternal summer; no Angel attacks or Evangelions needed. Shinji is shown to be living with his uncle, traveling to Tokyo. The only evidence of Third Impact left are petrified versions of the Mass Production EVAs, regarded as little more than bizarre ruins by everyone.
Shinji runs into Asuka at the train station, but she keeps it ambiguous whether she recognizes him. Shinji seems to be the only person to have any memory of the world as it was. This Shinji isn’t the same, however; rather than being marred by loneliness and afraid of everything, this is a version of Shinji who has found hope and a reason to live.
The manga’s ending is highly controversial, with some fans intensely disliking the “reset button” effect, essentially undoing the entire story in the last chapter. Others feel that it’s too much of a happy ending for Evangelion, and that as a result it misses the mark in a way the other endings don’t. Still, the manga’s ending has its fans, who believe that the better, more in-depth character development of the manga justifies this happier ending.