Kaworu 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.
It explains how Kaworu always has those creepy comments toward Shinji