Six possible answers to whats happened.
1. The aircraft depressurised, but continued to fly
This would explain the initial change in altitude and heading, as well as subsequent lack of communication, but not why the ACARS and transponder were turned off.
The transponder can be turned off from the cockpit and is done routinely when an aircraft lands.
Turning off the ACARS is more complicated, though, and would need someone with systems knowledge going into the aircraft’s avionics bay - but this should have been prevented if security was adequate.
If the plane was depressurised, it would continue to fly automatically until the fuel ran out.
The effect on passengers would vary depending on the altitude. If the aircraft was above 35,000ft, it would take about one minute before everyone was incapacitated.
Oxygen masks should have descended automatically which would work for around 15 minutes.
The flight crew could have lasted longer using their oxygen masks, depending on whether they used pure oxygen or an oxygen mix.
SUMMARY: Possible.
2. The aircraft was overcome by toxic fumes
The pilots should have been able to send out a distress call and, again, it does not explain why the ACARS and transponder were turned off.
SUMMARY: Unlikely.
3. There was an onboard fire which damaged the communications systems
This would explain the lack of communication, but it is unlikely the aircraft would have then continued to fly as long as it did if the fire continued to burn.
The aircraft’s communication systems could have also been disabled by power failure or sabotage.
Birdstrike is possible, but is unlikely to have caused such damage.
SUMMARY: Unlikely.
4. The aircraft was hijacked
The aircraft was not flown to another destination, nor was it used as a weapon for a suicide terrorist attack.
If it was an individual hijacker, then no one person or motive has been established and, if it was a group, no organisation has claimed responsibility.
SUMMARY: Possible.
5. The aircraft was deliberately diverted by the pilot/co-pilot
No reason for this has been identified. If it was a suicide attempt then why did the aircraft continue to fly for so long?
Another question is why there were no mobile phone calls or texts from passengers or cabin crew, given the in-flight entertainment (IFE) map would have shown the aircraft going off course.
One explanation is the IFE system was turned off.
The second is most passengers were asleep or did not realise anything was wrong until it was too late to do anything. If they tried to phone later, the aircraft would have been in a remote area over the ocean where there was no signal.
The third is passengers and cabin crew may have been incapacitated in some way, such as by hypoxia due to cabin depressurisation.
SUMMARY: Possible.
6. Simultaneous failures
One technical expert pointed out that for every plausible scenario, there is at least one contradictory statement.
"If it was hypoxia, then who turned the aircraft?" he asked.
"If it was a fire, then how did it continue flying? If it was the flight crew, then why did the cabin crew not intervene?"
He suggested that, perhaps, more than one scenario occurred simultaneously - such as a wiring fire and depressurisation.
OVERALL SUMMARY: Until more evidence is found, nothing can be proved.