He basically loses the battle against Ganondorf/Ganon in the Fallen Hero Timeline, though some fans seem to have a hard time grasping this concept. Frankly the Hero of Time Disappears timeline is the one that baffles me since this is the ending where Link does defeat Ganondorf, so how come he's still around in this timeline?
If this Link has been asleep for a hundred years, do you think he's a previous Link then, or still a new one?