I've been waiting all month to post this (ever since the advance screening in New York). Nothing here is based on spoilers post-Episode 2 and those of you who've seen ALL the spoilers can determine whether this makes sense or not:
(apologies for length)
What do the Silence want? What’s their end game? Well, as revealed in The Pandorica Opens, what they’d really like to do is to take control of the TARDIS and use it to wipe out all of time and space. But, as any fool or Dalek will tell you, “Only the Dok-tor can pilot the TARDIS!”
Well, the Doctor and River Song. Seems like a strange thing for the Daleks to miss, right? Well, we’ll come back to that later.
Anyway, the Silence want to take control of the TARDIS, but they need a Timelord to pilot the TARDIS, so they’re going to have to get one of those too. And how will their Timelord learn to fly a TARDIS? Well, they better make some practice TARDISes as well. (See Lodger, Impossible Astronaut.)
But wait, wait, wait! How do the Silence even know about the Doctor or the TARDIS?
Well, it all began in 1969, when the Silence abducted a pregnant Amy Pond. Who was she? Where did she get her strange, futuristic phone? Who are her friends? Who is this Doctor? What’s a TARDIS? How did the Doctor die? As they get more and more information, the Silence hatch a plan.
Take control of the TARDIS. End the universe.
If only they had a Timelord! Well, they don’t have one, but they do have Amy who is (a) pregnant and (b) a time traveler. Timelords are time travelers, but most time travelers aren’t Timelords! Still, we know from Flesh and Stone that simply BEING a time traveler changes you. “Good, isn’t it?” said the Doctor. Well, maybe not.
So Amy’s baby isn’t naturally a Timelord, but they can do a thing (let’s call it “quantum destabilization”) to turn a time traveler fetus into a proto-Timelord. As a consequence, Amy is both pregnant and not-pregnant. And they release Amy, and Amy immediately forgets all of this.
Sometime later, Amy is ready to give birth/not give birth and a post-hypnotic suggestion kicks in. She winds up back in 1963 or thereabouts, where she tells the Silence everything and happily hands over her baby. She even poses for a picture before she does! The Silence can’t believe their luck, because from their perspective, none of this has happened yet. But even so, a good “end the universe” plan is a good “end the universe” plan! No point in arguing.
So they raise Amy’s daughter at the creepiest of all creepy orphanages, and eventually it gets shut down for being TOO CREEPY! But they keep Amy’s daughter (and Mr. Renfrew in case anyone comes around asking questions).
So the Silence spend the ensuing years training Amy’s daughter to fly fake TARDISes and using a specially developed spacesuit to “incubate her Timelordiness”. Amy daughter doesn’t develop any long term memories through this period, but she is loaded with LOTS of post-hypnotic suggestions.
Number one: Next time you see the Doctor, kill him!
1969 rolls around again and Amy and company show up again and seem to scrobble the Silence’s plans, and in the chaos, the girl escapes. No worries, say the Silence. All part of the plan! The girl wonders aimlessly, not sure who she is, and getting progressively weaker without her incubation suit. After six months of this, her body gives out, and she regenerates for the first time.
Post-regeneration, the girl’s in a bit better shape. She’s stabile now, and starting to form an identity. But she still has all these post-hypnotic suggestions in her head. Including one that says she should recover that suit of hers and hide in a lake in the year 2011 and pop out and kill the Doctor. And there’s even a Silent on hand to make sure it happens the way they planned (and Amy told them it would happen) all those years ago.
Amy’s memory becomes her daughter’s post-hypnotic suggestion becomes reality.
Over time, those childhood post-hypnotic suggestions push Amy’s daughter in new directions: She finds a way to become a time traveler AND a doctor. Sound familiar? And she finds a way to infiltrate the Doctor’s inner circle by assuming the identity of one of his known associates: River Song. River Song who the Evil Alien Alliance overlooked, because River Song shouldn’t exist. She’s a paradox designed to pilot the greatest spaceship in all of time and space. She is…
[drumroll, please]
…an Impossible Astronaut.
And in the year 2010, on a day written into the base code of the universe, SAYS RIVER, River takes control of the TARDIS and uses it to destroy the universe, while a voice THAT ONLY SHE CAN HEAR keeps crying out “SILENCE WILL FALL!” A voice she’s carried with her, without knowing it, since her earliest days.
There’s good news: Though River essentially KILLED the universe at the end of THE PANDORICA OPENS, the Doctor figured out a way to bring it back. But now that River has killed the Doctor, can the Doctor figure out a way to bring himself back? Find out in Series 6 of Doctor Who!
(Note that this theory isn't helped tremendously if later in the season the Doctor fights the Silence in 1963 and accidentally gives them some of his DNA. That'll allow the Silence to hatch this plan in 1963 instead of 1969 and then to inject Amy with Doctor DNA in 1969 to make the baby more Timelordy. But I have no idea if that happens or not.)