Neon Genesis Evangelion is infamous for its ending, and what some call the poor depiction of the Human Instrumentality Project. The television series takes a very avant-garde approach and focuses on a first-person psychological account of the instrumentality process from the perspective of its main characters (primarily Shinji Ikari). However, its heavy use of abstract imagery and psychoanalysis had left many fans stumped. Following its airing, the director Hideaki Anno faced a backlash from the very audience that made Evangelion a success. The ending became so unpopular, Anno and Gainax studios were subject to hate mail, vandalism, and even death threats.
While some fans continue to believe the television ending to be a clever approach to end one of the most innovative shows to date, it is not difficult to understand why it was unsatisfying to the audience at large. The series by design asks many questions, but fans had hopes that its conclusion would answer at least some of them. Instead, they were treated to an ending that not only left all those questions unanswered, but asked new ones. Adding salt to injury, the ending itself was seen as inconclusive since it could be interpreted in several ways.
Because of this, the ending is often subject to criticism and is thought to be the result of budget under runs rather than artistic expression. While there are good arguments to support this theory (Gainax has in the past had considerable financial difficulties), Hideaki Anno has always stood by his decision to end the series the way he did.
The first sequel to Neon Genesis Evangelion is the 1997 theatrical film Death and Rebirth. The first half of the film is a summary of the television series. While producers may have thought this to be necessary, fans often see the film as sub-par due to its large amount of reused television footage. The second half is a retelling of episode 25 of the series. The poor reception of the television ending urged Gainax to tweak and re-release it. It begins at episode 25, but instead of turning to a rather narrow first-person account of the Human Instrumentality Project, it continues to tell the story from a third-person point of view. While moderately successful at the box office, Death and Rebirth still did not offer the ending audiences craved, instead ending in a cliff-hanger.
Several months later The End of Evangelion hit the theaters. To fans, the film held the promise of finally concluding the series in a way they deemed worthy. Just as Death and Rebirth, the film was composed of two halves: the first being episode 25 (which was released previously as part of Death and Rebirth), and the second being an all-new episode 26. Unfortunately, the release of The End of Evangelion, while amazing in scope, did nothing to end the debate over its conclusion. Because of the ambiguous ending of the television series, fans to this day remain divided over whether the film is a retelling of that ending, or if it is an alternate ending.
The television series ending has always been a subject of debate due to its highly interpretive nature. The series ends with Shinji Ikari in a dark room as he debates his place in the world. Eventually he is witness to an alternate reality where he does not have to be an Evangelion pilot, where his parents are both alive and Asuka Langley Sohryu is his childhood friend. Upon seeing this, he realizes that it is okay for him to be there, and at that point the walls and the world around him cracks and shatters. This is followed by heavenly-like scenes where Shinji is surrounded by the entire cast as they congratulate him. For the first time Shinji is seen happy.
All this takes place in Shinji's mind during the instrumentality process, and the scenes are symbolic. The room is Shinji's AT Field which he uses to distinguish himself from others (in effect isolating himself). Shinji's choice is a point of contention. Some see the shattering walls as the breakdown of his AT Field and his acceptance of instrumentality, upon which he becomes one with the rest of mankind in the form of Lilith. Others see this as a rejection of instrumentality.
While in the television series Shinji's choice is left ambiguous, in The End of Evangelion he clearly rejects the instrumentality process. The film then concludes with the death of Lilith, leaving Shinji and Asuka on a post-apocalyptic beach.
Adding to the confusion is the fact that The End of Evangelion contains several scenes also seen in the series. For instance, in the series a scene with Ritsuko Akagi's dead body floating inside Terminal Dogma is clearly shown, even though the events leading up to her death are not seen until the films. Thus, the events of The End of Evangelion are not entirely unrelated, and do up to a certain point coincide with the series. They are simply told from different perspectives.
Depending on one's interpretation of the television series ending, the plot diverges with Shinji Ikari's choice to either accept or reject the instrumentality of mankind. In the series, the decision is left ambiguous, and may be interpreted as Shinji accepting Instrumentality, where as in the theatrical films he outright rejects it, believing it to be synthetic.
To understand the ending of Evangelion it may be useful to briefly look at its creator, Hideaki Anno. From any film maker's point of view, the chance to explore an alternate reality or ending presents an enticing opportunity. Remakes are in fact very popular in Japan (take the Gundam series for example).
It is also a well known fact that following the poor reception of the television series ending, Hideaki Anno became disillusioned with the Otaku culture (death threats have a way of doing that).
Some fans see the theatrical films as Anno's way of getting back at that culture. While he would give the audience the apocalyptic action scenes they wanted, there would be a price to pay; and that price came in the form of the Human Instrumentality Project. And so while to some the series may have had a confusing but nonetheless happy conclusion, the films show the alternative.
It may however be presumptuous to declare the television ending a happy one. In both cases, the world is destroyed and mankind is returned to a sea of L.C.L. The difference is Shinji's choice, which results in either a unified mankind in the form of Lilith, or the destruction of Lilith, thereby allowing mankind another chance at life. Neither choice is right or wrong, it is simply a choice. Those who love overanalysis may also claim that Shinji's rejection of a unified mankind may be symbolic of Anno's disillusion with his audience and his rejection of the Anime culture. But I am not brave enough to overanalyze Anno; you may try that at your own peril.
Ultimately, the television series offers an ambiguous ending that may be interpreted in several ways, which ironically is how Anno prefers it. Meanwhile the theatrical films take a less liberal approach to conclude the story, which is what fans have been asking for. Matt Greenfield of ADV Films (the North American distributor of the Neon Genesis Evangelion television series) explains the series and films do indeed have distinct endings, but they were both prepared simultaneously like the two possible endings of a video game.