Pilot suicide by a long shot. There is no other alternative theory that comes even close.

What was interesting is to see them piece the theory together from the very fragmentary and little evidence (what is even more mind-blowing to know how little evidence there was to play with given we are talking about a 747).

The true mystery left is how did he execute the suicide and why. How did he dispatch the co-pilot? (There was a very small window to do so). What did he do in the final hours (was he alive for the entire duration)?