We've all heard both sides of the story. There are two types of people... ones who despise the end of Neon Genesis Evangelion and others who respect it for what it is. The fans of this series are practically split down the middle on the issue in endless debate. With that big of a divide Hideaki Anno decided it was time to replace the end which he himself was not even pleased with.
Forgetting the final two episodes ever happened, The End of Evangelion picks up after episode 24. Shinji finds himself at an all new low after killing Kaoru and Commander Ikari is still at odds with SEELE. Asuka still lies in a comatose state as an all out assault on Tokyo-3 begins. Elite soldiers attempt to hunt down and kill the Eva pilots sending Misato desperately running to find Shinji. Asuka is placed in Unit 02 which is dumped into the lake while Rei has gone missing.
This 90 minute ending is divided up into three episodes to symbolize it as a replacement for the original. The same voice actors reprise their roles for the main characters which is a huge plus, however it seems that some of the lesser characters have different voice overs on the English dub. Furthermore, for some odd reason they pronounce "EVA" differently from how they did the whole series, putting the stress on the V rather than the E. This doesn't ruin the whole film but it is quite odd.
From the beginning it doesn't take long for things to heat up as it features one of the best fights in all of Evangelion. Finally Ms. Soryu is done justice after being overshadowed by Shinji throughout the entire series continually getting her butt handed to her time and time again. Asuka snaps out of it and is able to sync with Unit 02 again bringing out her fiery attitude in full force as she dominates in a spectacular display of piloting skill.
Most importantly, EoE serves as a far more reasonable ending than its original not only because it actually continues with the storyline, but also it continues the dark path the series was progressing in by the end of the 24th episode. The language is harsher and there is a lot more gore than normally found in any episode. There are also some scenes that are pretty disturbing, especially the opening scene which you will have to witness for yourself.
The symbolism in this film is abundant and it should not be watched unless you have seen the first 24 episodes of Evangelion. Otherwise you will find yourself lost and most likely will not appreciate the story. It also helps to have a fundamental understanding of the Christian religion, but that is not necessary.