After getting mind-raped by Arael, Asuka is completely broken. She is so grief-stricken she quits being Supergirl, and thinks she will also lose her EVA pilot job...which, in her mind, would turn her into someone worthless.
Gendo Ikari Mind Rapes his own son with the Anti-Life Equation. He spends a few chapters in a deep coma, with Asuka worried sick about him and, while he gets back through The Power of Love, he admits by the epilogue that the Equation left some pretty deep scars on his psyche.
During the End of Evangelion portion of the story, Gendo Ikari unleashes Doomsday. Yes, that Doomsday. Rei tries to stop him and gets curb-stomped so thoroughly that Asuka thinks for a second that she's dead when she encounters her, and as for Asuka, she suffers what you would expect in the eventual battle, and Shinji was Forced to Watch part of it. And the subsequentIt Is Not Your Time drama.