The creepy, white Silence dudes were always ruling the Universe by post-hypnotic suggestion. There are adversaries that were more powerful than the Time Lords. Ex - The Osirians
Pyramids of Mars.
OR
Creepy, white Silence dudes came vie a known event. Either the crack through the Void (
Army of Ghosts) or when the Master helped to pull Gallifrey from the Time Lock (
The End of Time).
The creepy, white Silence dudes are "way out of their time" (
The Day of the Moon).
On the fields of Trenzalore, at the fall of the Eleventh - The Doctor battles these dudes, wins
but goes through a regeneration.
The creepy, white Silence dudes begin to realize they are losing on the fields of Trenzalore. They go back in time (or
Back to the Future) to kill the Doctor. Thus they alter history. History will have none of it. "Time can be rewritten. Not all of it" (
The Impossible Astronaut)."See what happens when you try to change history" (
Let's Kill Hitler). "Time can be rewritten but, not all at once" (This season's exploits). Hence, the utterance of Dorian's Head, with an ere of disbelief, "The Sentinels of History". Only their history as the rulers of all.
The are responsible for blowing up the Tardis. They took control during a dream state (
Amy's Choice). Those white beads were a projection of them (not little white mice
). They knew Amy was going to be the Doctor's companion. This was their first attempt to alter history.
The creepy, white Silence dudes knew Amy and Rory will conceive a child in the Tardis. They kidnap the child to use as a weapon against the Doctor. Their second attempt was in the warehouse. The third was at the lake.
But, something went wrong. A crack in the fabric of time and reality opened in Amelie's bedroom. The Universe poured into her dreams. All of reality revolves around her not the Doctor.
That's how I see Moffat's Whovian World.