CNN just now - Captain WAS a checkpilot!

That explains why there wasn't an additional pilot to oversee the newbie 1st officer.

The thing that is the human element STILL is this:

How can we rule out the possibility that "Alright, goodnight" wasn't calmly said by the captain or first officer just before the captain took his rest break? (which would be against company rules, surely, when flying with a new copilot) The rest break would have been VERY routine for a flight of that duration, especially at night.

Captain rests first. Lights out in cockpit for sleep. Newbie would have been fiddling with controls as refresher, but in the dark. Easy to accidentally mess things up. CNN had said that 1st officer "was transitioning to the 777" after completing simulator training. Two to two 1/2 hour rest break on that duration flight before time to wake capt and switch. Lots could have accidently - or on purpose - have happened.

Copilot knew that captains made the takeoffs and landings. When would be his turn? When the capt was asleep! He turns off the autopilot to get the feel of the aircraft. All goes to hell in a handbasket after he messes things up, and when the capt is finally awake, there was not enough fuel to return to their original route.

Not a very exciting explanation, but a simple one. Malaysia Air surely wouldn't volunteer that the newbie was left unsupervised in the dark!

Despite elaborate alternatives being suggested, I still am not ruling this out entirely. I've seen just too much in my day. Once the other Pan Am purser came out of the cockpit and said "I flew the plane! I flew the plane!" Stuff happens. But nothing as sad as this other than Lockerbie.