I just rewatched the six episodes. Such a freaking good show! I still don't understand it all. But I won't comment about all that. I just wanted to speculate out loud on the cliffhanger ending to season 2. I think there are three clues as to how he did it.
1. i think there is something to the hanging dummy at the beginning of the episode.
2. an obvious choice: he asked molly for her help but we don’t know the details.
3. he was very adamant about watson not moving from the spot he was at as they talked on the phone and then a bike messenger hits watson after he jumps, knocking him loopy for several seconds.
The actor who portrayed Moriarty was absolutely brilliant. The way he could change his face, tone, and body language was incredible.