10 Dropped Doctor Who Plot Threads We'll Never Get Answers To
6. The Whereabouts Of The Kovarian Chapter
Madame Kovarian was the big overarching villain of Series 6, and along with the Kovarian Chapter, she was responsible for turning River Song into a murderous psychopath, resulting in the Doctor's "death" on the shores of Lake Silencio.
In finale episode The Wedding of River Song, Kovarian was killed by Amy Pond in an act of revenge, which seemed to put an end to her once and for all. But then, the events of this story were wiped from continuity when the timeline was aborted, meaning that Kovarian (and, presumably, some of her Kovarian Chapter followers) is still running around out there in the Whoniverse, possibly plotting another evil scheme.
Now sure, villains get abandoned all the time in Doctor Who, but Kovarian had such a raw, unbridled hatred for the Doctor that it's really hard to believe that she'd just leave him alone, especially after discovering that he was still alive.
However, Kovarian was a Steven Moffat creation, and since he's no longer with Doctor Who, it's highly unlikely that we'll ever see her return. Not that other writers can't reuse villains, but Kovarian was so intrinsically tied to Moffat's Series 6 arc that it would feel really weird to have someone else try and pick this thread back up.