The pilot had a plan for revenge. He initiated the plan, then got cold feet, set the plane on auto-pilot and killed himself (hypoxia). The plane ran out of fuel over the Indian Ocean and crashed.
I have no idea how to fly plane, but if he turned all the communication ‘systems’ in the plane off, would this have affected his navigation? People are too reliant on technology now in general - would a young pilot (the other pilot) struggle to reach his target (Petronas Towers, or Bombay perhaps) without communication with the ground? He could have simply spent Saturday morning searching for Land in the Indian Ocean before running out of fuel