I believe the Big Bad this season is the great intelligence. He's been in two (maybe 3) eps this season. He also may have been the one that controlled, and subsequently exploded, the TARDIS during the Pandorica arc.
We're seeing some throwback to "The Silence will fall...question asked...Doctor who?" The Silence wanted to take the Doctor out to prevent him from revealing his name. Now that Clara knows it (albiet she was mind wiped, it could still be there), the Silence may come after her. There is also a plot line from a novel where the Daleks create a perfect companion for the Doctor to lure him into a trap. I believe the G.I. created Clara inorder to learn the Doctor's name.
We also know that River will return at some point this season.
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