I am reposting this here because another poster asked for it:
My theory: The Pilot is known to be a strong political supporter of an opposition politician - Ibraham, whose "guilty to charges of sodomy" conviction was reinstated earlier on the same day as this flight. Meaning he can not participate in an upcoming election which some sources report he was bound to win.
The Pilot has seen bribes and corruption within his country. Earlier this very day he saw how corrupted the judicial branch is. He has long observed various corruptions and bribes within the airline industry, including cargo not being examined, passports being stolen and sold.
The Pilot had a friend - another pilot - over to play on the flight simulator a few months prior. That friend made an offhand, sarcastic remark, "Hey, things are so corrupt, even the military is compromised. I'd bet an unknown plane could cross our country and the military would never even know it!"
This thought sticks in the Pilot's head. He begins to wonder if this could really happen. He starts to play on the flight simulator, working out a plan as to how something like this could possibly happen. It is an intellectual challenge for him to "play this game". He eventually figures out a potential flight plan for something like this to happen. This is all just a "game" to the Pilot. But it is a fun game for him to play. He plays it over and over again.
The afternoon of the event, he becomes very upset when he learns that his chosen political candidate is going to be put back into jail. All hope is lost for changes to take place in his beloved country, to end the corruption.
He reports at the airport for duty that evening. He learns his co-pilot is to be the guy who was recently reprimanded by the airline for breaching cockpit safety by having females in the cockpit during a flight. This does not particularly please him. He is not in a good mood anyway. He and his wife had an argument before he left home earlier that evening. She accused him of spending too many hours in front of his flight simulator.
The flight takes off. The co-pilot is young and wants to engage in idle chatter. The Pilot is not in the mood for this. The co-pilot persists. The Pilot is rude to him, telling him to be quiet. At that point, just to see if anyone notices, the Pilot turns off the transponder. No one notices anything - not even the co-pilot. The pilot makes the last contact with ATC, saying "Alright, good night" instead of using the normal wording for sign-off. Once again, no one notices or acknowledges this was a deviation from protocol. The Pilot thinks to himself, "It really is as bad as I feared".
Next, the co-pilot says he must leave the cockpit to visit the toilet. By protocol, he is not supposed to leave the cockpit at this time. Anger floods the Pilot, as he realizes how lax both performance and discipline actually are within the Malaysian airline industry. He gives a curt nod, "Yes" to the co-pilot.
This is when the pilot turns off the second communication system. In his anger and frustration, somehow "the game" begins. The Pilot enters the well rehearsed coordinates of "the game" into the autopilot.
The co-pilot returns to the cockpit. The Pilot tells him he has just received directions to divert the flight due to ground problems. He tells the co-pilot that he has already programmed the needed changes into the autopilot. That they may need to return to the original airport. The co-pilot does not question this. The Pilot instructs the co-pilot to make a calm announcement to the passengers about the diversion. "Assure them there is nothing wrong with the plane" he says, "just say there is some ground problem." The co-pilot follows instructions and makes the announcement. This pacifies the passengers and the flight attendants.
The plane then turns and passes back over Malaysia. The Pilot wonders if he will be picked up on radar, if fighter jets will suddenly appear outside the cockpit window. None appear. Now the plane has begun a series of preprogrammed turns.
After some time, the co-pilot finally wonders why they have not received any further instructions from ATC. Because they are now far off course. He suggests the Pilot call in to ATC for updated instructions. The Pilot says no, he does not want to do that, they are fine, they will just wait to hear from ATC.
At some point the co-pilot FINALLY realizes something is very, very wrong. He attempts to call ATC but gets no response. Nothing! He turns to the Pilot and asks "What is going on? What have you done?"
The two men begin to struggle. The co-pilot attempts to manually take control of the plane. The plane ascends steeply, then descends sharply. Finally it regains altitude and levels. The Pilot sat passively in his seat as the co-pilot struggled to control the plane.
The Pilot realizes what he has done. He has played the ultimate game. As the co-pilot busies himself reprogramming the autopilot in order to get them back home safely, the Pilot calmly reaches out and shuts off the oxygen supply to both the cockpit and the cabin......
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I am probably going to change some things. And I invite anyone else who wants to add or subtract to feel free to do so.
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