The most likely scenario is the simplest one. The comms mast on the underside of the fuselage separated from the plane in flight. There seems to be a known weakness due to improper use of adhesives and there is supposedly an AD for this issued by the FAA. With the mast gone there is no comms and there is a small hole in the fuselage. The cabin gradually decompresses and incapacitates the crew. They attempt turn back and program the autopilot to descend, then go to sleep. The plane goes down to 3,000 feet, levels off, and flies into the Indian Ocean until the fuel is exhausted.
The passports, cell phones, hijacking, accidental shoot-downs are just conjecture. The fact is the comms mast has been found to have cracks and probably just fell off.
There is nothing on a 777 called a comms mast. There are vhf antennas, hf antennas, tcas antenna, satcom antenna, no comms mast though. These antenna are attached with fasteners, not adhesive. If one did depart the aircraft the “hole” uncovered would not be a pressurization challenge for the two massive engines to compensate for.