We've been following 'Sherlock' these days & at the end of Season 2, here's what I'm convinced of: Sherlock knew all along what Moriarty's plan was - hence the mannequin hanging from the ceiling in the first (or was it second?) episode; and Sherlock suggesting the high-rise as the place for their final meeting. I'm also convinced that the twist has something to do with the (garbage?) truck parked below the building when Sherlock jumped & Molly's job in the morgue (or is she in forensics? - either way, she has access to corpses).
Just an instinct.