Rat Hole
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Rat Holes are small busts in the wall that serve as homes to rats in The Wind Waker, Phantom Hourglass, and Spirit Tracks.
Appearances
The Wind Waker
If Link tosses some All-Purpose Bait in front of a rat hole, a rat will come out and offer to sell him something. Potions and All-Purpose Bait are the most frequent wares sold by these rats. However, whenever there are rats around, that doesn't always mean there is a rat hole in the area, as seen within the Submarines floating about the Great Sea.
Phantom Hourglass
Only four of these holes appear in game, and they come in pairs. A rat holding a small key will appear from one hole and run to the other. In order to get the key from the first rat (located in the Mountain Pass on Mercay Island), Link must push a block in front of one hole, then, once the rat runs to it, corner it. In order to get the key from the second rat (located in the Temple of Fire on the Isle of Ember), Link needs to kill it while it is running from one hole to the other.
Similar holes also appear, however, and serve as doorways only accessible by Bombchu and Gongoron.
Spirit Tracks
Rat holes make another appearance in Spirit Tracks. They are occasionally seen in the Tower of Spirits. If a rat comes out of its hole and is seen by Phantom Zelda, she will cower in fear until Link defeats them. Rats will keep coming out unless Link pushes a block in front of their hole, thus preventing another escape.