Aloha Whovians of the web. I came up with a theory about "Time Runs Out":
As we all know, the Doctor died in the Impossible Astronaut. From spoilers on Doctor Who Tv about episode 13, it is set in an alternative time line. My theory is that when the Doctor dies in America, the skeleton with the sonic in hand is the Doctor's, the sonic in his hand after being hidden up his sleve while being shot. As he burnt and sunk, the sonic, being alien, survived and floated into his skeletal hand. After his death, time unravels. Rory is truely erased from the universe after killing Amy, or his Auton has been melted and reformed. The Romans carry in through time, Winston Churchill's Dalek contant kept him alive and pterodyctals and mammoths survived without the Doctor's intervention. River's data ghost would have also been deleted. None of our time crew in this time line. But then it restarts, giving us the young Ponds.
That's all for now dragonnets!