Replace Kouta with Shinji, and Lucy does not split into Nyu. Starts before Shinji meeting Asuka, but after the 5th angel has died. It's a first shot at a story, hopefully you'll like it

Lucy has escaped from the Diclonius research and detainment facility. Her destination, Tokyo-3. Nothing will stop her from her goal. Not the military, not NERV. Not even the messengers of God are going to stand between her and a quiet life with the boy she loves. But even when all of her enemies are dead, the blood on her own hands could prove too great an obstacle to overcome.

Humans learn from their mistakes but what if that mistake kills them? Humanity is under attack from forces they couldn't even begin to understand. The fate of humanity, angels, and diclonii lays in the hands of children while forces scheme from behind the scenes. The era of humanity is about to end, will a new era for humanity rise or will it be forgotten. Do they deserve to live?

Rei ayanami pics up Lucy on the way to hell. Lets see what happens, shall we?