No story so far except "you're a new mutant and your power allows you to bonk anybody in this game (except Xavier)".
I think Oni, at the very beginning, planned to gradually complete Rogue sex scenes (at this time, he also talked about getting better at coding and using Ren'py, which is hilarious from today's perspective) and then flesh the game with some story around those two characters, the MC and Rogue.
Then he added Kitty - and don't take it the wrong way, I really like her - and everything went down hill: the game became a flight forward in the harem genre. Since then, the cycle has gone on and on: UPDATE - add a new girl without actual sex content, UPDATE - add her BJ/HJ/TJ poses, UPDATE - add her penetrations poses, rinse and repeat. And if it weren't bad enough, Oni usually doesn't concentrate on one girl at a time but has multiple ones at various stages along this cycle.
Today, I don't think this game will ever be "finished", let alone get a story. It will be an ever-growing collection of sex scenes with characters from Marvel (since Oni can't even stick to the Evolution show, although there is no shortage of sexy female mutant in it; odds are we are getting damned Gwen as the next character...).