Ok, so the events of OoT happen, Ganondorf's sealed inside the Sacred Realm/Dark World. Link is sent back into time by Zelda, which creates 2 timelines. The one is the place where he left, ruined by Ganondorf's rule. The other was his childhood. I think he told Princess Zelda about the dangers of the future, and Ganondorf was going to be executed. It's seen in Twilight Princess he didn't die because of the Triforce and was banished to the Twilight Realm. Then they have peace...and leads to Twilight Princess. Oh ya then Link leaves to continue his adventure in Majora's Mask.
In the other timeline, the one he left, Ganondorf somehow came back and began destroying and burning again.

In the timeline where he was sent back, centuries come on and Twilight Princess comes in. For those of you who have played TP, you know what happens.
As for WW, the story goes on and continues in PH.
What do you think?