I thought the moral dilemmas you presented in the first half of this and in the second were interesting, though I wasn't convinced that Jack would ignore all his training and knowledge and try to change history. He would know the consequences are always worse than what he's trying to avoid.

But with the rape you lost me completely, I'm afraid. I'm not a fan of non-con and violence anyway, but I can see the logic for it in fics about the Master, for example. Quite apart from any disquiet about portraying rape as entertainment, the thought of Jack raping the Doctor... no. Not even when he's very angry and hurt; I just don't believe he's capable of it and I couldn't read past that. Sorry. It's a pity, because I did think you had an interesting premise.