Almost all the conjectures have been quit exotic and very imaginative, which coincidentally keeps the interest alive and boosts TV ratings and acts as click bait.
The delays in turning off the transponder and the data stream to the modem, flying between way points on a well known path etc might be explained by confused and disabled pilots too.
Hypoxia can set in as little as 90 seconds of oxygen deprivation and will severely incapacitate and confuse people. Cabin pressure loss is the most common theory for hypoxia. But cabin pressure loss would deploy oxygen masks, sound alarms and the pilot would have been alert in the first few seconds to declare emergency and radio out. The captain seems to be nerd with home made flight simulator, he would have reacted correctly to oxygen masks dropping from the ceilings.
Carbon monoxide is a way for hypoxia to set in. If there was a slow smoldering fire in the cockpit, not hot enough to trigger fire alarms it could result in incapacitated confused pilots. Again there are CO detectors, and warnings and associated with it.
I am not sure how regularly these systems that detect cabin pressure loss and CO detectors are tested. It is quite expensive to actually deploy all those oxygen masks. So even the regular testing protocol would require the maintenance crew to disable the actual deployment of the oxygen masks and test the detection and deployment signals. They could forget to turn them back on, like the did in the Helios flight disaster I mentioned in another thread. CO detector is chemical based.
They have to be replaced regularly and this is an old plane.
Once the pilots flip switches on and off in confused state lose their consciousness completely, the plane would fly on autopilot following the way points that happened to be programmed.
If there is foul play involved, it would be worthwhile exercise to make sure every flight plan that was file in that duration and every flight directed by the control towers in that time is legit and locate those planes. The pilot(s) could easily turn off the transponder, drop out of radar, pop back in and start using a different call sign. Without a transponder, air traffic control completely trusts the pilot to self identify the plane correctly. If the malefactors had filed a fake flight plan, the plane could change its identity mid flight without attracting attention.