"Silence will fall when the Questions is asked." Dorium Maldovar says the Question is "Doctor Who?". After Oswin's memory hack, the Daleks are now asking the Question.
Daleks are all about hate, and destroying the Doctor. The Silence is a militarized religious order dedicated to hating and exterminating the Doctor. The Headless Monks, the Anglican Marines: seems like there are a lot of militarized religious orders in the future. Could the Daleks be responsible for this?
At Demons Run, when Amy is "ready to pop", we see something resembling a Dalek eyestalk monitoring her. The Headless Monks believe the domain of faith is the heart, and the domain of doubt is the head, so they chop off their own heads. The Doctor's favorite weapon is the head; he always thinks his way out of trouble.
River Song was in Stormcage in 5145, which is approximately the time that Captain Jack comes from originally. Liz 10 was still Queen in 5145, about 2000 years after "The Beast Below". River acquired a vortex manipulator from Dorium Maldovar in 5145 so she could meet the doctor when the Pandorica opens. The Silence is responsible for the Pandorica. Madame Kovarian and Colonel Runaway consulted Dorium shortly before the events at Demons Run, so presumably Demons Run also occurs in the mid-5100's. The Weeping Angels have a massive presence at the crash of the Byzantium, which occurs during River Song's incarceration at Stormcage, and the Anglican Marines exist during this time as well; again we're talking about the mid-5100's. Captain Jack's time. I'm sure I heard a rumor that Captain Jack is retuning for the 50-year anniversary.
Could the Time Agency be where the Tesselector came from? Could it be that Captain Jack was originally assigned to the Tesselector? The Time Agency wiped two years of Jack's memory, which is the reason he quit the Agency. Also, that memory alien tampered with Jack's memory.
A lot of memory tampering is going on: Oswin and the Daleks, Jack's memory, the Crack erasing the memory of the Universe, Amy's memory restoring the Universe, "The Beast Below" erasing memory of the starwhale that Starship UK is built upon. Psychic paper and perception filters also relate to memory tampering.
The Dalek Emperor went mad and began calling himself God of the Daleks. Dalek Kahn went mad while penetrating the Time Lock, and acquired new emotions that led him to judge and condemn the Daleks. Dalek Sec became a Dalek/Human hybrid and thereby acquired human emotions. The lone Dalek in Henry van Statten's collection in 2012 acquired human emotions from Rose Tyler, aka Bad Wolf, and committed suicide in the end. When van Statten fires employees, he has their memory wiped.
The common threads seem to be Daleks, memory, militarized religion, and the mid-5100's.
