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For over a year now, we've been hearing onscreen that River was imprisoned for killing someone who she considered very very important and a great man.
Here's my thought as to who it might be:
Rory...not the Doctor - not only would that be too obvious (everyone thinks he's all-important)
while I haven't gotten to see the recent eps (nothing since the pirates), that speculation was based on something I hear was revealed this week recently:
River Song is Melody Pond, daughter of Amy and Rory.