Spoiler What Happend to Navi? (may Want to Have Beaten Oot, Begun Majoras Mask)

[axelsoraroxas]

You remember in twilight princess when you go through the gate of time and find a hidden temple? The window that navi exits through is the same window that leads to the hidden temple in TP.
It's possible she lived out her life in there and never actually left the temple at all.

 

[-KingJason]

What is in the exact window Navi flew through? Well in TP, it is the temple of time dungeon. Just sort of a conspircy of some sorts, but I doubt Nintendo didn't mean for tat to be just a coincidence.

 

[Graboidfan31]

I think that Navi most likely just went back to wherever her home was.

 

[Majora's Soul]

I know!! Since Link went back in time before the temples and events, there was peace because of the changed future. Since there was peace, Link didn't need a fairy then, so navi never came.

 

[Skunk]

Well, it's possible that after going through the window, navies was split into two parts, Tatl and Tael.