The Silence, a religious sect of the space church called the Papal Mainframe, Doctor Who. It’s hard to imagine how that is possible when the TARDIS, the time machine that doubles as the Doctor’s home, shouldn’t have been that easy to destroy. While it was confirmed that the Silence was responsible for blowing it up, the series has yet to address exactly how the villains managed to do it.
The Silence themselves didn’t actually appear until season 6 of the series. They were arguably some of the most fearsome creatures in the show’s history, with long, gray faces and no mouths. Whenever the Doctor and his companions, Amy Pond and Rory Williams, happened upon them, they would instantly forget the Silence’s existence after looking away. Throughout Doctor Who season 6, the Silence was intent on killing the 11th Doctor to stop a prophecy that stated the Time War would resume when the Doctor revealed his true name. The Silence went to great lengths to keep the Doctor from answering this very question that mirrored the title of the show itself. The creatures even went so far as to kidnap Amy and Rory’s baby, who grew up to be the Doctor’s wife River Song, in a bid to brainwash her into doing the deed on their behalf.
The Silence’s destruction of the TARDIS in season 5 is one of Doctor Who’s greatest mysteries. During the episode “The Pandorica Opens,” the Doctor is imprisoned inside the Pandorica, a box created to hold him, in a bid to prevent him from operating the TARDIS at the exact time it’s supposed to blow up. After all, it was believed that no one but the Doctor could control the time machine. If he wasn’t inside it, then the logical conclusion was that it couldn’t explode to cause the cracks in reality thereafter. Problem solved, right?
But, despite the Doctor being inside Pandorica, the TARDIS blew up anyway with River Song inside. Long story short, locking the Doctor up was a trap all along, most likely put in place to keep him from getting to the planet Trenzalore, which is where the prophecy states he’s to reveal his name. But, how did the Silence one-up him">the powers of a Time Lord because she was conceived while inside the TARDIS. That could explain why she’s able to operate the time machine with such ease.
However, she was also brainwashed by the Silence. It’s possible that she was responding to their deep-rooted persuasions to bring about the end of the universe by detonating the TARDIS’ self-destruct mode while it was flying inside the time vortex. While River had already left the Silence’s order by then, an old trigger could have caused her to do something to blow it up. This would explain why she was inside the TARDIS at the time of its demise, bringing the Silence’s plans to fruition. At least for a while. Doctor Who may never answer this question, but so long as the show goes on there's hope.