Nahhh.. Flight software was probably altered even before aircraft left the ground and at some point, no matter what the pilots did it had no effect. The guy flying the plane was probably sitting in the passenger section via his laptop or perhaps in another country flying the aircraft remotely. Commands by the pilots were probably futile as they were locked-out completely. Part of the evil hack probably included killing their voice communications from the cockpit to ATC after ‘alright, good night’. You buyin?
Surely the pilot can take back manual control in such a situation. A plane hack?
Opening scene from For Your Eyes Only
Not even remotely likely.
The 'altered by computer' being bandied about in the press is much ado about nothing. All aircraft of this type have computerized navigational / flight plan systems. Saying that MH370's flight plan was altered by computer does not suggest that a passenger, a remote engineer or even the pilot was using anything external to commandeer the plane.
What it does suggest is that the plane was 'hijacked' by the captain, with or without consent and aid from his First Officer. It suggests that after MH370's transponder and ACARS were tampered with (also pointing to the pilot) and the aircraft changed course instead of continuing into Vietnamese ATC cover, it continued to fly for some time and execute a planned flight path. It did not change course and fly aimlessly, as might have happened if depressurization, smoke or some other catastrophe incapacitated the crew or if a passenger had stormed the cockpit and commandeered it and began to 'fly by wire' as the 9/11 story goes.
The pilot(s) decided to disable as much of their aircraft's electronic signature as possible then changed course and entered new electronic waypoints into the navigation system, thus changing the flight plan. Their motives, destination, and whether they reached it are what's in question now. If the speculation about briefly climbing to FL450 are correct, that does suggest a conscious plan to kill the passengers and cabin crew - and perhaps the FO as well.
Altering a flight plan in such a way is not an extraordinary event in itself. Weather, air traffic, fuel concerns or even a medical emergency on board an aircraft can result in a captain altering his flight plan. Of course, this is done with the knowledge and consent of the airline and ATC. Doing it own your own after cutting communications and heading off to an unknown course with unknown intentions IS extraordinary. But having this happen points suspicion sharply at the captain, not away from him.