The transponders failed either as a result of the fire or due to the pilots pulling fuses to try to quench the source of the fire.
The proper action if that occurred would have been to declare an emergency and make a 180 back to the nearest airport, Sultan Mahmud (TGG), which has an 11,417 foot asphalt runway perpendicular to the shore, a distance of only 111 miles.
Instead, no mayday, and they turned west and flew a meandering path until they went off the military radar.
We know from the Inmarsat data that the airplane continued flying until sometime after 0811 KUL time. It's likely a fire would have destroyed the plane before that. Inmarsat also believes it flew south, although that conclusion seems on somewhat shakier ground.
My best guess is some combination of Flight 93 and Payne Stewwart / Helios 522. They were hijacked. Perhaps the captain locked the copilot out of the cockpit and headed for Pakistan or Somalia. He turned south to avoid military radar in India. Then there was a struggle to retake the plane. The captain depressurized the cabin, figuring he'd survive on the cockpit oxygen. But his simulator didn't have a way to practice that maneuver, and he botched it, putting himself out as well as everyone else on the airplane. Then the autopilot flew the plane south until it ran out of fuel and went in hard.
One intriguing detail that has recently come out is that the copilot's phone, which was verified to have been turned off at KUL, contacted a cell tower in Penang, although no call was placed. Perhaps, when the copilot was locked out, he turned on his phone intending to put out a mayday, but there was no service. Then, when service briefly became available, he was too engaged in the struggle to notice.
As for the CVR, it's unfortunate that it only records the most recent two hours. That will likely be quite boring, the interesting parts having been overwritten by engine noise and a big splash.