One of the most beloved character's ended up on the receiving end of the worst possible treatment.
While the Evangelion franchise itself — with its gloomy mood and overburdening melancholy — is rightfully considering to be one of the most prominent representatives of a 'darker' anime genre, The End of Evangelion is generally agreed upon to be the franchise's own metaphorical darkest point — and in more ways than one.
Originally spawning not out of the author's desire but rather out of Gainax's attempt to please the fans, dissatisfied with the original ending, The End of Evangelion rewrites the infamous episodes 25 and 26 that concluded the 1996 anime.
But while those episodes, despite being filled with a bunch of cryptic and meaningless nothingness, did imply some kind of positive outcome for the story and its heroes — The End of Evangelion prefers to end its story on a much more darker and pessimistic note while, at the same time, brutally murdering pretty much all of its characters and providing no satisfying explanations to any of the series' countless mysteries.
And while many fans would readily argue that this is not necessarily a bad thing, as the film's nihilism does ring true to the anime's core themes and ideas, there's no doubt that the tale of The End of Evangelion is just as beautiful as it is tragic. With the saddest part of it, undoubtedly, being the death of Asuka — an arguable soul of the series, one the most beloved and least melancholic characters of the main roster — who ends up on a receiving end of the worst possible treatment.
She spends the trail end of the original Evangelion struggling through a tough psychological crisis that, at a certain points, leaves her almost a husk of her former self. But, unlike Shinji, who never truly overcomes his numerous issues, Asuka emerges out of this battle victorious — with both a rediscovered will to live and a massively checked ego.
This is the state that The End of Evangelion inherits her in — and what does it do with her? Pits Asuka against nine Mass Produced Evangelions with seemingly impossible odds.
And then, once she — through an unbelievable combination of determination, grit and her newfound will to live — defeats them, the film robs her of the victory, allowing her enemies to regenerate first and then brutally eviscerate her Eva, murdering the pilot.
Thus, the only character who was capable of doing something meaningful in the story at that point, is not only killed, but killed in a devastating fashion after having accomplished nothing, ultimately rendering her sacrifice meaningless. Many fans tend to compare Asuka's death to that of Misato, but that is hardly a fair comparison — as Misato, before finally succumbing to her wounds, does manage to save Shinji, which means that she did not die for nothing.
Asuka's death happens at around the midpoint of the film serves as an ultimate loss of hope — with her gone, the rest of the characters are left defenseless against the SEELE's onslaught and have nothing to do but to gradually succumb to their fate.