1. Restatement of the "Reverse Chronology" Theory
It may have gotten a little confusing back there, so for the conclusions sake, lets assemble a rough timeline: Starting with The Angels Take Manhattan, The Ponds are gone due to an incident with the Weeping Angels. (Rory first, then Amy, because she loves him so.) Losing them both has The Doctor so upset, he goes back in time and visits them at several points. The first point is during The Power of Three, where he tries to get them to go on a couple more adventures with him and theyre content with homelife. Eventually, they jump back into the time and space faring saddle (upon the insistence of Mr. Williams) and they wind up in A Town Called Mercy. Once mercys concluded, The Doctor and companions encounter the Dinosaurs on a Spaceship, and eventually winds up at the Asylum of the Daleks. With the end of Asylum, The Doctor gets a warm and fuzzy ending for himself as he says goodbye to the Ponds and says hello Oswin Oswald, his new companion. At least, thats what it looks like. Again, Steven Moffat might be laughing upon reading this article. In which case, well be able to hear it echoing throughout the land. With that laughter will be the chilling revelation that no matter what we hypothesize, no matter what we guess and check, Moffat will always have something up his sleeve that proves us dead wrong. In which case, it's not too late for Whovians to assemble upon said tower and shake their fists in the air, with a cry of "MOFFAT! GIVE US YOUR SECRETS!".