Watched the final episode on iplayer.
Apparently there's a big debate going on about how it happened.
Obviously Molly is involved. And the cyclist knocked over Watson. As this happened, a rubbish lorry drove past so it is theorised that the cyclist was to distract Watsons attention while Holmes jumped into the back of the rubbish lorry to cushion his fall, then from there to the pavement. Prior to jumping he could have taken some drugs to slow his pulse, (Watson checked it). The ambulance crew were in and out very quick without waiting for any other emergency services turn up so these were probably arranged by Molly too, and then she could have faked all the paperwork, as she is meant o be a forensic pathologist or something.
Other theories include the body really being Moriarty with some clever mask on, but that is very unlikely, my guess is that Moriarty also comes back from the dead next series.
Overall, a good watch.