All the evidence points to a hijacking by the pilot, with or without the assistance of others aboard.
Problem: Motive. WHY???? From there, my GUESS is that he intended to land the plane safely and hold the plane & passengers as chips to bargain for the freedom of jailed Malaysian dissident Anwar Ibrahim. That’s my guess as to motive.
His plot was successful to the point of last (publicly reported) radar contact, but ultimately he crashed. Either ran out of fuel, or failed to execute a difficult landing, or was shot down by a sovereign that is afraid to admit it, or lost control of the plane to others aboard.
He did not pre-warn of his intentions lest the plot fail, he did not want to add to Ibrahim’s woes.
That's not a bad guess. It's possible that he intended to land at Cocos Island off Australia but over shot it and just decided to ditch the plane instead.