I thought an on board fire might have been a possibility, I believe an exact cause was never found for the
Egypt Air 777-200ER ground fire in the cockpit that was fed by the crew oxygen?
However I don't see the possibility that the fire was so intense that it disabled acars, transponder and comms (but not the autopilot, or the power to the inmarsat unit that replied to pings), incapacitated the crew and the passengers but then somehow self extinguished and allowed the aircraft to keep on flying for another 6 hours?
That's my two cents on that particular theory anyway.
On a slightly less related note, the Aviation Safety Network posted an interactive map that shows the courses of all
88 aircraft that have disappeared without a trace since 1948 for anyone who missed it.