So, in Clara's 101 places she is missing 2 years in her countdown, 16 and 23.
Now what if this is not just a mistake, this is when she previously travelled with the Doctor (assumedly at some point between A Good Man Goes War and Asylum of the Daleks)?
Something horrible happened in that time, which resulted in the Doctor losing his memory and Clara splintering.
Someone is trying to bring them together again, making her say the phrase Run You Clever Boy and Remember, in order to try to trigger his memory (as the Doctor tells Amy if something is remembered, it can come back)
This may in turn link back to the other mysteries of the season, as we know the Silence can themselves alter memory and the TARDIS explosion fragmented across all time.
The only thing we're not sure on is who is bringing them back together. My wife thinks the great intelligence, I think it is the androgenous figure watching UNIT at the end.
What do people think?