Well, I've always assumed it was a double-bluff of some kind, making someone think he was dead when really he wasn't. Before I thought it was the Silence, but then we quickly saw they were horribly underwhelming. Dealing with these weird people makes sense, though. And his resignation would make sense as the Flesh, because he really would be dying, rather than pretending to die, which doesn't quite fit his quiet demeanor.

That's true, the love triangle is ridiculous, and now that we know that he's in some way attached to her daughter, maybe that will break away...

But on that subject I would love to see some "You keep your hands off my daughter" moments from Rory. Or, possibly, him confronting the Doctor over the fact that he swooped in and screwed up the lives of his wife and his daughter (man, the Doctor should feel lucky Rory doesn't know what happens to her)

Well, Stephen said she remembered because she was special, or something like that...but that still doesn't explain how she exists. Her entire existence is contingent on the Doctor existing, she literally has no life without the Doctor, so...how was she there?