First of all, I enjoyed that episode. Really. Ok, unlike what seems like most of tumblr, I knew that Sherlock wasn't going to die... A) there's a season 3, and B) it's Moffat, for crying out loud. So maybe the emotional impact wasn't quite there. Still, though, I thought it was very well done-- I like the cooky cinematography, Moriarty was delightfully psychotically creepy, and the twist where Sherlock's own team (although not John, never John) turned against him was unexpected but compelling, and very realistic.
The thing is, though...
I've got no idea how Moffat's planning to fix this one. This isn't Doctor Who, we don't do body duplicates-- there's no way it was anyone but Sherlock who stood on that roof, and therefore there's no way it was anyone but Sherlock who jumped... we even saw the apparent corpse's face. Right?
So what am I missing?
One thing I'm very certain of: Molly is the key. Sherlock asked her to do something; we don't know what. Furthermore, when Moriarty prompted Sherlock to name his only three friends, he named Lestrade over Molly. My assumption there was that Moriarty was waiting to assign the assassins their targets based on what Sherlock said-- obviously, he wouldn't have fallen for John and Mrs. Hudson being left off the list, but the third entity was a wild card. So, Sherlock pins Lestrade and, in doing so, keeps Moriarty's focus off of Molly.
But to what end? What was she doing? What could she have done?
The only other clue I came up with was those funny puncture marks on Sherlock's neck in the final scene, when he watches John at the grave. Some kind of injection?
It's very much Moffat's style to skip the crucial explanatory scene-- he did the same thing in The Wedding of River Song. The problem here is that I have literally no ideas. (I'm sure a lot of people on the Internet have come up with loopholes, but I wanted to get my thoughts down before stuffing my brain with other people's ideas.)
EDIT 2/7: Something to do with that bouncy ball? Whatever happened to it?
In short: