We'll never see the telemetry, but maybe there is something we can understand looking at when MM93's crash happened.
In fact he crashed when, after a few fast laps, Rossi visibly slowed down -- it seemed he wanted to let Marc in front, but MM93 didn't want to -- so he also had to slow down. The rear tire of his Honda of course cooled down a bit in the process, and maybe he lost that little bit of concentration. Then maybe engine braking or whatever did the rest, but as a secondary cause to a loss of tire temperature.
It's all a conjecture of course, but it's a possible explanation. When the tires have trouble staying at the proper temperature, slowing down can be more dangerous than going fast. It's a difficult balance, -- especially when your speed is dictated by the rider in front. Rossi managed to solve the wet setup equation best, as was apparent already during warmup, and so he won. Petrucci (also announced at warmup) was on the old Ducati that notoriously has a lot of rear traction (too much on the dry, but just perfect on the wet), he used that characteristic well, and arrived second.