Every time Haytham and Connor have sex, Desmond comes out of the Animus completely churned up. The worst part is that this starts to affect his relationship with his own father. Every time Bill pats his shoulder or touches him in any other way he remembers Connor doing it with his father and gets agitated/tries to look away/steps aside. It keeps getting worse to the point where he can't have a normal conversation with him or even look at Bill anymore.

Whether Bill knows about it all or is completely clueless is up to anon. It doesn't need to be Bill/Des either, it can be just Des feeling uncomfortable about it all, but not necessarily feelings. Whatever floats your boat~