I would not dismiss the Helios theory all together. Explosive decompression takes out some of the kit in the E&E bay, including transponder and ACARS, most pax and crew incapacitated. Some survivor gets on portable O2 and gains access to the FD. They try to push a few buttons but don't know how use the radios or fly the jet. They try a few turns and climbs and descents, typing stuff into the FMC, eventually portable 02 runs out and the jet continues on last track until fuel exhaustion over the indian ocean. Even with the autopilot off a 777 that remains in trim should remain airborne without any inputs for many hours. I don't fly the 777 but relevant questions would be : is transponder (1 or 2) in the same bus as essential kit that drives the ACARS, is the pax O2 in the same bus? what would happen under a variety of electrical malfunctions if appropriate actions where not carried out by the crew? for example loss of essential batt bus. There are sure to be combinations that take out all comms (even if some could have been regained by the crew if they had been able to).
It seems more plausible than a super elaborate suicide plan. I could (try to) understand a suicide as an act of madness but going for hours and hours dodging radar to take 200 souls with you to a far away oceanic grave. It seems far too elaborate and contrived.
As an act of terrorism it also seems contrived. if you wanted a big jet to carry an evil deed later on you could buy a big one in Russia while keeping a pretty low profile. If you wanted a high profile why has nobody credible claimed the action?
Technical and human factors explanations must be completely discarded before going down the "James Bond villain" routes