Ok. This is just a theory, and while I'm sure the high heejuns at Gallifeybase have already worked out that the series will revolve around the Master, Rani, and Metebelis III spiders based on the fact that the Doctor wore a watch in 2010... I dont care. I want this theory putting down now, so that if I'm wrong it will be long forgotten by then, but if I'm right I can point at it and say "HA!"
Here goes...
If you payed attention you would remember that the events of the Big Bang replicated many of the events of 11th Hour. Including the key meeting of The Doctor and little Amelia, during which Prisoner Zero escaped and went and hid in Amys spare room. (We know it was at this point and not earlier because of the door opening and closing). OK, so in 11th Hour the Doctor came back to save Amy but was a little (12 years) too late. However the Atraxi came and captured Prisoner Zero so all was well... Now here's where the theory starts.... The Doctor coming back followed by the Atraxi obviously DIDNT happen, otherwise the wedding guests would have known that he wasnt imaginary... With me?
Now this means that Prisoner Zero escaped, but was never caught. What happened to him then?
My theory is... that when River Song was fannying about in the TARDIS and landed in Amys garden on the eve of her wedding, Prisoner Zero was waiting and hopped on board where he also started the explosion process to blow the Universe up, knowing that the Doctor would do the only thing he could, and sacrifice himself to reverse the process, at which point Prisoner Zero was free to escape.
A cunning plan... But how could Prisoner Zero know that all this would happen I hear you ask...
Ahhhh! There's the rub! When the Doctor crashed the Pandorica into the TARDIS exlosion he started the rewinding process, and started going back along his own Timeline.... and he uses this event to stop off and tell little Amelia a bedtime story which later makes her remember him, and bring him and the TARDIS back...
Well... what if, at the same time as he was doing THAT, Prisoner Zero was doing the exact same thing. but he went back and told himself exactly how to escape the Atraxi prison... In an almost ironic use of the self same paradox that The Doctor used to escape the Pandorica!
So who IS Prisoner Zero eh? Well, lets look at the clues.
Shape shifter...
Can control the TARDIS...
Can navigate the reverse time part of the explosion...
Knows the Doctors methodology, and uses it to his advantage..
Dangerous Criminal...
My best guess? OMEGA... Or another Timelord gone bad... We HAVE seen the Master assume a slimey snake form, but that was the TV movie so I try to forget it...
I know what some people are thinking... "but he's a slimey snake thing..." Ahhh but is he?
Steven Moffat is a master of Smoke and Mirrors. At the end of 11th Hour we only know that what we are looking at is the appearance Prisoner zero took when he appeared to Amy in her house at the start of the ep. The Doctor assumes thats his actual form... He doesnt have anything to base that assumption on, so is quite possibly wrong. Who says Prisoner Zero doesnt have a menagerie of species tucked away somewhere like the coma ward of Leadworth hospital?
So... where is all this heading?
Clues we've been seeded both on and off camera:
River Song kills the greatest man she's ever known, a hero to many...
The end of ep 7 cliffhanger will be a "game changer"
Moffat said when we find out about the Silence plot, we will all realise that we have "known from the very beginning"
The voice in the TARDIS saying "Silence Will Fall" occured just after River left Amy's, and due to the fact that the rest of the Universe except the museum had gone bye bye, suggests that the owner of that voice ws indeed IN the TARDIS...
So I reckon, with nothing but intuition on my side, that the following will occurr, or something like it anyway...
About episode 5 or probably 6 next year, a scene will occurr in the TARDIS where the Docotr has to go of into one of the other rooms, and will pop back some minutes later... At that point he will be replaced by Prisoner Zero, who puts him into the coma thing. I dont knowif the audience will be made aware of the switch at THAT point, but it will lead to the end of ep 7, where River will either appear out of the blue, (or suddenly turn round, if she has already been in the episode) and shoot the Doctor dead. If we havent been told about the switch, then that will be the resolution in the next short season in Autumn. But if we HAVE been told, or given enough info to work it out, then "another" doctor will step out from behind a pillar or something and say something like "Ha, bad luck Doctor Song... you shot the wrong one... I'M Prisoner Zero" or "Omega" or whatever....
Leading to a cliffhanger where either way, we are left thinking River has shot and killed the Doctor...
Thats the bare bones of it, and I know its a bit long winded... Thoughts anyone???