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.
For some of the bee colonies, the workers and the queen have genetic relatedness of 0.75, our body cells have r=1 between blood cells and gonads. Thus the insect colony is a looser agglomeration and our bodies are tighter agglomerations. Between parent and children the relatedness factor r=0.5, between cousins r= 0.125. uncles/aunts to nephews/nieces r= 0.25. In societies where first cousin marriage is encouraged, the general relatedness of the population could be much higher. Though it was not unknown in Europe (Einestein, Darwin married their first cousins) it is more common in the East. Even then most of them allow only children of a brother and sister to marry, not children of two brothers or children of two sisters. The only exception is the Ottoman empire which made marriage between children of brothers legal/halal/kosher. (Since Ottoman empire was Islamic many people confuse this practice with Islam. But in Muslim countries that were never ruled by the Ottomans this practice is very rare). Places that were once ruled by the Ottoman empire you could have whole villages or clans where all males have exactly the same y chromosome and have very high degree of relatedness. Such populations would pledge allegiance to the clan and take great personal sacrifices for the sake of their clans or tribes or villages or their shieks.
You could see the level of personal sacrifice made by individual animals or cells as a continuum plotted on genetic relatedness factor r. Our cells pledge very tight allegiance to the germline cells, ants/bees somewhat looser, human societies with very high relatedness have high patriotic feelings and personal sacrifices for the sake of community.
Trying to impose a western style democracy of a society with a mean value r on to other societies with an order of magnitude different r would not work easily. Giving autonomy and self governance for people/tribes/clans with high degree of relatedness, but subject to collective punishments and rewards would be considered sacrilege in the West. But such practices are more likely to succeed, pacify the population and lead to peace.
After I land, I don't know what I would do with 239 - X number of people in Kabul or Bangladesh.
Credit for the inspiration: When I was in sixth grade I read a comic where they steal ships. A submarine releases a fog of anesthetic in the path of the ship. One person on board uses oxygen cylinder to escape. When everyone has fainted this guy, radios out claiming to be a different ship (Campbell Cross, I still remember the fake name) coming in for assistance. Meanwhile the pirates board the plane, secure the crew below the decks, repaint the ships name. Radio out saying there are np debris, no ship to be seen. Participate in the grid search and then slink away. The tamil name for the title is "kaatril karaintha kappalkaL" , or ships dissolving into thin air. It was translated from some British comic book. I don't know the name of the original in English. The heros who solve the mystery are Lawrence and Judo David. Can any one help find the original?
It is possible somehow both pilots lost control of the plane and it flew on auto pilot, following whatever route was programmed into it.