The timeline still remains fuzzy and the occurrence of events in what order is pretty important to having some idea of what happened. Right now indications seem to be that left-turn and the reprogramming of the flight computer came BEFORE the handoff call to ATC. Again, in the "gap" between controllers which would be potentially a good time to "go missing." So if this is the case it could rule out the possibility of the diversions being due to an emergency because if that were the case then the plane would have had opportunity to give its intentions and any problems to ATC so help and aide could have been provided. Still a lot of questions in all of this and, really, the timeline could be the key to what happened. If the turn happened AFTER the last contact with ATC then the loss of the transponder, ACARS and turn could all be due to some-kind-of onboard emergency that necessitated some-kind-of diversion to the nearest capable airport. (The scenario proposed in the Wired article above.) If the turn happened BEFORE the last contact with ATC and it was around this time the transponder and ACARS systems were lost the emergency scenario seems less likely given that the pilots had the ability to contact the ground to let them know of the emergency. Either verbally or by putting the emergency code into the transponder, or both. Still and again a lot of questions.