An explanation to the Gainax Ending of Gakuen Datenroku...SPOILER WARNING! When Kaworu sacrificed himself to save Shinji from being eaten by Yggdrasil, he decided to either reset time or send Shinji, Auska, and Rei to another universe, where the craziness of Gakuen Datenroku didn't happen and where the three could live a happier life. Unfortunately, because Kaworu was eaten by the tree instead, he could not join them.
Another Explanation to the Gainax EndingKaworu have fused with Lilith, and therefore becomes God instead of chosing not to. Using his newly (re)obtained Divine Powers, he Altered Reality so Rei recovers, NERV no longer exists, along with abunch of other minor stuff so that Asuka, Rei, and Shinji are all happy. As a bonus, he contacted the other remaining Angels and told them they can continue their earthly existence in peace as long as they don't do anything funny. Or else he'll use his Deus Ex Machina Powers to punish them. He can do that because he's God.
This is the Kaworu's origin story for every other EVA universeIt explains how Kaworu always has those creepy comments toward Shinji