Up to this point, Neon Genesis Evangelion has depicted themes surrounding "the human heart" and "communication between people" through the stories of the main characters. However, the climactic episodes, Episode Twenty-Five "The World Ending" and the Final Episode "The Beast That Shouted Love at the Heart of the World," reverse the relationship between the story and the theme. What would normally be considered the story is kept to the bare minimum and "the theme itself" is told. The material is theoretical and experimental, and without a doubt, something never seen before in TV animation. When it originally aired, it became an incredibly hot topic and divided the fans in their opinion.
The conclusion to the drama and illuminating the mysteries. In response to fans clamoring for those two things, it was decided that there would be a remake of Episode Twenty-Five and the Final Episode. The result of that are Episode 25 "Air" and Episode 26 "A Pure Heart For You," which were released as the theatrical "The End of Evangelion."
Thus, the story of Eva would branch into two stories with the diverging point being the end of Episode Twenty-Four "The Final Messenger." The two stories each unfold differently and arrive at their own climaxes. Episode Twenty-Five and the Final Episode tell the theme directly. And the other version, Episode 25 and Episode 26, depict the same, following the story. It is not that one is the complete version and the other is incomplete. Just like the multiple endings of a game, two different endings were prepared for one story.