"I think it depressurised and the pilots passed out trying to return to KL."
Putting everything together, to me this seems the most likely scenario. It doesn't explain why the ADS-B transponder dropped out, though, unless it was somehow damaged in the 'event' that caused the depressurisation.
If I think off the top of my head for an explanation, there are a couple. I've seen that an Oxygen Bottle is located close to the avionics bay. If this blew up (happened once before on a QANTAS 747 - DH saw the aftermath on a business trip to the Philippines, where the aircraft diverted and was repaired - everyone got away with that one!) it could puncture the fuselage and wreck the avionics.
Second could be a fire that progressively burnt through different systems on the aeroplane including the cables to the many and varied antennas. This happened on a Swissair flight that, unfortunately, did result in a loss to the aircraft. Another accident, to a freighter, happened when a load of lithium-ion batteries also caught fire (called a thermal runaway). They are banned now as air cargo but every iPhone and laptop has one. If something like that were to be in someone's luggage, depending what was around it the aircraft's onboard firefighting equpiment may not be able to cope.
There are so many scenarios with so many different possibilities contained within them.