Exactly. Since very early on, all the evidence has pointed to one horrible scenario: the Captain committed a premeditated act of murder/suicide by incapacitating the passengers and other crew, then flying south (probably until the aircraft ran out of fuel) and either ditching or impacting at speed from height into the ocean.
And to address the matter of incapacitating everyone else on the aircraft, it would have been a reasonably simple procedure - and one which is wholly supported by the available radar evidence. The Captain would have got the First Officer out of the flight deck (either because the FO left to go to the bathroom, or because the Captain invented some reason for the FO to go back into the main cabin). Once the FO was out of the flight deck, the Captain ensured the door was locked (and also disabled the transponder, and very probably pulled the circuit breakers on the CVR and FDR), disabled the cabin pressurisation system, and then took the aircraft up to its operational ceiling height. The oxygen masks would have dropped down in the cabin, and the cabin crew (and FO) would also have had access to small bottles of oxygen (enabling them to stay portable). But those oxygen delivery systems would have expired after around 15 minutes. By contrast, the flight deck emergency oxygen system lasts much longer - in most modern airliners they can last for hours (and indeed US regulations, for example, demand that pilots wear oxygen masks constantly if the aircraft is above 25,000 feet and only one pilot is on the flight deck).
So, with the aircraft at around 40,000ft, and with the cabin pressurisation disabled, the available emergency oxygen in the main cabin would have run out within around 15 mins. After that, the passengers and crew (including the FO) would have had no choice but to breathe the depressurised air - whereas the Captain would still have been fine on oxygen in the locked flight deck. Humans breathing in air at 40,000ft pressure simply cannot get enough oxygen to function, and they pretty quickly (within 5-10 mins) succumb to the effects of hypoxia: they would have become drowsy and confused, then gradually fallen asleep, then fallen into a coma as their brains became oxygen starved, and within a further 15-20 mins they would have lapsed into irreversible brain damage.
So within around half an hour, the Captain would have got himself into the position he wanted: every other person on the aircraft - including the FO - would have been entirely incapacitated and probably effectively brain dead. The Captain could now bring the aircraft down to whatever altitude he chose, and either repressurise the aircraft or keep it depressurised and continue to wear his oxygen mask.