Well, it sounds like the breakdown and hatesex would be Chell’s lowest point in the story, so the only place to go from there would be up. Either she comes out and tells Wheatley exactly how much of an asshole he is for stabbing her in the back and then forcing his way back into her life and acting like everything’s okay, or she realizes that she can’t go back to being alone so as long as he isn’t intent on causing her harm, she might as well make the best of things, even if it means letting go of her grudge and her righteous anger. And from there the relationship begins to improve, either because she has decided to be less hostile and more receptive to Wheatley’s companionship, or because Wheatley’s making an effort to be less of a douche in order to fulfill his promise to take care of her. Also, you got rid of Space early in the story before he had a chance to do anything significant, so he really should be brought back in some capacity. His relative innocence could soften Chell up until she develops a friendship with him, which teaches Wheatley, through observation, how to be a better friend himself, or attempts to wrangle the hyperactive little guy could give them something else to focus on beside their animosity, causing them to let their guards down more. Another way you could go is have him die or be badly injured as a result of the two neglecting him to focus on their own issues, leading to Wheatley blaming Chell because she didn’t care about Space, just like how she didn’t care about him when he was almost killed, while Chell blames Wheatley because Space was his responsibility, not hers, and that leads to more lashing out at each other and then becoming vulnerable and needing each other to deal with the incident. I also recall that the original prompt mentioned Wheatley (and Space) teaching Chell how to speak AND dance. You’ve already started the speaking thing with Wheatley being an asshole and trying to be a “savoir” to her so he can feel good about himself for HER accomplishments, so maybe a part of them growing closer comes from Wheatley re-approaching the subject more altruistically, and from there you can add dancing and any other number of skills and passtimes that make Chell feel more alive and human.
Of course that’s if you want if you want a standard happy ending. You could also have Chell decide that she can’t spend the rest of her life alone or with someone she hates either way, and so she decides to go searching for humans again, which means there’s no reconciliation and Chell’s ultimate fate is ambiguous, but there can still be some hope that Chell does find other humans and ends up happy with them while asshole!Wheatley ends up alone.
These are all really interesting ideas, and I like them even if I wasn’t intending to go in those directions. I do know that I didn’t want the story to have a “happy” ending in the sense that Wheatley becomes “good” (or as good as he ever really was, which is debatable. he was a selfish twat from the beginning, just nicer about it) and they have a normal romance.