Originally Posted by Leven Six

Signed up because Skylark made me.

Now, this is the story as I see it, since he likes the way my portion of his theory works:

Suppose, as Sky suggests, the timeline does split again. That is, there is two of everything. The Hero Link warns Zelda, and Ganon is imprisoned. At this time, Rejected Link is still in the Kokiri Forest. However, since the Deku Tree is unaware of what is going on, as would Ganondorf prior to the time travel, the Deku Tree is still cursed, and still assigns Reject Link the Mission to save the world.

So the stream just within the timelines is:

HoT Link warns Zelda
Reject Link is somewhere in the Deku Tree

Now this is where it gets tricky:

Hero Link has nothing to do, and Navi leaves. Hero Link, realizing he could never keep up on foot, takes Epona and goes after her. However, since R. Link is still thinking he needs to get the M.S, he goes to see Zelda as per the Deku tree's instructions.

At this point, the timestream looks like this
Hero Link triggers events of MM
R. Link goes off to see Zelda.

Now I'm sure Zelda has realized, or at least guessed, that there are now 2 "Link"s within the timeline. Therefore, she assigns R. Link a new task: to protect the Four Sword if a time arises that requires him to do so. Any information, including Zelda's befriending R. Link (I'm calling him FS Link from now on), is entirely up to speculation. One theory I propose is that Zelda doesn't realize it at all and proceeds to assign him the task, but when it comes time to pull the sword he can't. Ergo, Zelda assigns him the Four Sword task, while Ganondorf, realizing his path into the sacred realm is now gone, hunts down the trident. Later, the seal does weaken and FS Link goes and activates the events of FS and so on.

Timestream for Hero
Back to the past, explanation and arrest, MM and traditional child timelines from there

Timestream for Preexisting Link
Begin as normal, get informed about Ganondorf, M.S., and Four Sword, Time and friendship, Four Sword events occur. Middle two being interchangeable.


Of course, I myself feel it's pretty solid, but if you have a contradiction in this explanation, be my guest.