What the heck happened to Navi?

I finished the game Legend of Zelda: Ocarina of time a while back and Navi flew away and I thought "I can't believe he ditches Link" so naturally I play Majora's mask next to find him (even though he annoyed the heck out of me) and so the game starts and it says something about finding an irreplaceable friend and suddenly I'm sidetracked by Skull kid and his gang so I finish the game and I was so disappointed that the Navi plot was never tied up! Help me out here what happened to that annoying thing?