Some clues point to connections between the Silence and Simeon's Whisper men. One, both species operate just outside the limits of human perception. But it could be said about many creations from Moffat ( the Angels, the Vastha Nerada, Prisoner Zero ... )Two, according to Mrs Kovarian, the Silence waged war on the Doctor because they thought he was dangerous, and Simeon/the Great Intelligence said as much. So could they be related ? Could it be that, by trying to kill the Doctor,Simeon and the Whisper Men screwed up badly, brought about exactly what they were trying to prevent,and the Silence had to clean up their mess ?
Which leads to the big question : the Silence went to great lenghts ( blowing up the TARDIS, kidnapping and corrupting Melody Pond ... ) to prevent the Doctor from going to Trenzalore. But now, he DID go to Trenzalore, someone DID answer the "oldest question in the universe", and ... well, what was the Silence exactly trying to prevent ? Could it be that there are severe consequences to the Doctor being attacked by the Great Intelligence, then entering his own timestream ?For instance, couldit be the events of "The Name of the Doctor" are what created John Hurt's "dark Doctor" ?After all, he's the only one Clara didn't "see", then didn't save from the Great Intelligence. MaybeSimeon corrupted him, and THAT was what the Silence was trying to prevent ... But you could argue that the Silence and their goons explicitly fear the NAME Doctor, a name John Hurt isn't allowed by his other incarnations to use ... In any case, I can't see how any of this could make "the Silence fall" ???
Here's my theory : the Silence has misinterpreted the prophecy ( we know how Moffat loves puns ). It's not "Silence will fall", it's "silence will fall". Meaning, if Eleven goes to Trenzalore and John Hurt's apparently war-mongering Doctor comes to existence, and is not stopped ( hello, "Day of the Doctor" ! ), all life in the universe could be reduced to silence ( either dead or dominated byapower-crazy, Time War-damagedTime Lord).
( Of course, you could always say Dorium's prophecywasn't fulfilled, since the one who answered the question was NOT a living being, then was able to lie ... )
Any thoughts ?