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Link supposedly makes a wish on it in the Sky Keep in SS, but I haven't gotten that far yet so I'm not sure what happens to it. In TWW, after the King of Hyrule makes his wish, the Triforce floats up and out of sight, though I'm guessing it returns to the goddesses or the Sacred Realm.

(Spoilers) In Skyward Sword, at the end, you can still see the Triforce in the hands of the Statue of the Goddess, this sets up the stage for the "Interloper War" in which many people lust after it. So, it could be said that after a wish is made upon it, it stays in the same place (as shown in the Decline Timeline, where there was a monarchy that used the Triforce in order for the prosperity of the Kingdom, each King who used it had a perfectly balanced heart), unless the person who makes the wish has an unbalanced heart, in which the Triforce will then split apart into three pieces, and each crest will lie within a person who represents the three attributes of the Triforce, best. After someone collects the three crests lying within each of these said people, the Goddesses will have no choice but to grant the wish of the person who touches it first. After this wish is made, it is apparently sealed away in Wind Waker by the Goddesses. Timelinesplitter 22:32, May 15, 2012 (UTC)