2 weeks after EoE, Shinji grew a spine leading to Asuka being able to reveal her feelings for him. She becomes a teenage mother 15 minutes later. Rei uses the knowledge she retained from her godlike state to covertly usurp Gendo and takes over Nerv (and eventually the world) herself, and pilots Unit 00 to school every day instead of walking. She also directs Nerv's research to finding technology to bring people back to life. Kaji is brought back to life, and he and Misato marry, Pen Pen being the minister who marries them. Kaoru accepts that Shinji isn't gay, but finds out that Fuyutsuki has a thing for teenage boys. Ritsuko is also brought back to life and also opens herself up to homosexuality with Maya. Yui is brought back to life, and she forgives Gendo for almost fucking humanity. Touji and Class Rep/Hikari get together, while Kensuke remains a virgin forever.
AND THEY LIVE HAPPILY EVER AFTER.