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I thought a better idea for the 3rd timeline is that Link created two timelines when he first picked up the mastersword: Adult and original child and the third timeline created by Zelda as the "new" child timeine that leads on to Twilight Princess

1st timeline is where Zelda sends you back to. As she sends you back to the point were you never opened the door of time. This timeline leads onto Twilight princess.
2nd timeline is what you start in and you created by picking up the master sword. Ganon's chasing Zelda while you're around in this timeline. You return to this timeline when you put the mastersword back to do spirit temple shiz.
This is the timeline you never return to though. The door is open ganon is free to get the triforce and this should be the "fallen" hero timeline.
3rd timeline is the adult timeline were you defeat ganon and seal him away.
Zelda sends you back to timeline 1 at the end of this. This timeline leads on to Wind waker