The passengers are most likely all dead.
I would have to agree the passengers are dead due to hypoxia. If the Captain did go on a jihad, without crashing the plane, and the First Officer was not involved, it would have been difficult but not impossible.
All he had to do is tell the First Officer he wanted something to drink and could he get it for him or tell him he can go for a stretch while he flies the plane. I do not know about this airline but I believe FEDEX requires one of its pilots to put on an oxygen mask, if the other pilot leaves the cockpit, in case depressurization occurs. So he tells the First Officer he is going to put it on, just in case and it does not look out of the ordinary.
Once the First Officer leaves, he lowers the cabin pressure, shoots the plane up to 45,000ft and flies the plane in an erratic way so it creates chaos in the cabin, to the point where the crew and First Officer cannot keep themselves steady enough to get to the oxygen equipment or get to the cockpit. At 45,000ft it takes lees than 30 seconds for people to die from lack of oxygen.
He was able to hold it at 45,000ft, long enough to kill everyone before it stalled, where at that point, it took some time and altitude to get it under control, hence the lower 23,000ft level, then rise back to 35,000ft.
Just my opinion that can be added to all of the others
Until I hear a better explanation, I am going with yours.