My assumption was that he went to Molly because she could "procure" a body and the night was spent "fixing" it. Notice that Sherlock made sure John stayed where he could see the roof and the fall from where he was standing, but not the ground where Sherlock fell. And then the bicyclist crashed into John, further disorientating him.

Amazing episode overall- I really wanted to hug John at the gravesite at the end. Poor, poor John.