In "Cold Blood," the Doctor explained that certain events represent "temporal tipping point[s]." How such a pivotal event plays out can "create its own timeline, its own reality." I believe that the Doctor's meeting with little Amelia Pond was such a tipping point. The Doctor was supposed to return to Amelia in five minutes, as he promised. His failure to do so created a whole new timeline, which we've witnessed over the whole course of this season.
Because this new timeline isn't supposed to exist, it's inherently unstable, which is why cracks keep opening in spacetime. The analogy here is to Donnie Darko, where the paradoxical appearance of a jet engine creates an unstable tangent timeline. Donnie must send the engine back into the primary universe before the tangent timeline collapses and destroys everything. As that analogy suggests, the Doctor must make good on his promise to little Amelia to save the universe.
But how can the Doctor do that when he's trapped in the Pandorica? According to this eagle eye, the Doctor has River Song's vortex manipulator:
My guess, therefore, is that the Doctor will somehow use this vortex manipulator to escape the Pandorica and travel back to the temporal tipping point. In so doing, he will reset events from that point forward so the tangent timeline ceases to exist, just like Donnie Darko.
