Personally, my explanation is somewhat based off of this guy's. The drawing the in the video also translates to my explanation, so at least give that a look.
My theory is that the three splits in OoT are due to Link's time travel. The first split is caused when Link travels between the present and the future. Obviously we all know that the future segment of OoT becomes the AT, however the present portion of OoT, does NOT become the CT. The CT timeline is created when Zelda sends Link back in time, creating a third split. The reason a second split is created and Link is not returned to the original timeline is because Link is not the one who sends himself back in time, Zelda does. And since Link no longer exists in the OT, no one is there to warn the Kingdom of Hyrule about his attack, nor is there anyone to rise against once he has taken over, leading into the original IW story from ALttP.
Essentially, my theory assumes that time travel is relative to the one who is commencing it. Link created the first split by traveling to the future, while Zelda creates the second split by sending Link to the past. Had Link done it himself, there would only be two splits, but since Zelda did it, it created a second split leading to the CT. The timeline expressed physically should like something like this:
OoT (present-game) - ALttP
OoT (future) - WW
OoT (present-ending) - MM
My apologies if this seems like incoherent rambling, since I'm not that awake right now.
Thoughts? Anyone else have their own substitute theory?
Edited by Master BiShredder, 09 July 2012 - 10:27 AM.