What on earth were they doing way down there???!!!
Good question - but it may never be answered.
The information released to date though, does gives us some idea and probably reduces the possibilities to three (to which there could be some variations).
One is that there was some kind of emergency (a sudden fierce fire?) to which the response of the pilots was to attempt to return to Malaysia. I dont buy that. Why? Because of the deliberate way the transponders were turned off at the point where they left Malaysian air control and moved into the area under Vietnamese air control. The autopilot had apparently already been re-programmed for the swing back to the west. The last message was from the co-pilot, in a cool, calm voice, acknowledging to Malaysian control that they were leaving Malaysian air space, but his "Allright, goodnight" did not follow the usual protocol.
From there the plane turned to the west, back over Malaysia and at some point turned south and kept, likely controlled by the auto-pilot until it ran out of fuel, the engines cut out and the plane went down into the ocean. If there had been an on-board emergency the possibility is that everyone was dead.
It does not seem to be likely (at least, in my opinion). So what are the other two options.
The second option is a hijack (or attempted hijack)
The third is a deliberate decision by one or both pilots to kill themselves and the passengers. A scenario that is so cruel and cold-hearted that it is almost unimaginable.
If we take the second option, you could consider little signs like the last (non-standard) response of the co-pilot, with a gun pointed at him, as an indication that the pilots were considering their options. Shortly after that last voice contact the plane (its said) rose to 45,000 feet. If the pilots de-pressurised the plane at that height, everyone on board would die, but the plane would continue on its programmed flight until fuel ran out.
Perhaps they considered that to be the way to cause least harm to the world.