Catacombs

In, the are a series of underground chambers that lead into the nether regions of the Clock Tower in Termina.

Overview
The Catacombs are only visited once during the entirety of Link's quest, serving as a pathway into the land of Termina from the Lost Woods. It is completely uninhabited and features only three rooms, the last of which includes a treasure chest containing Deku Nuts. Link accidentally wanders into the Catacombs after pursuing a masked Skull Kid accompanied by two fairies, hoping to retrieve his ocarina and horse from them. He enters a large tree and falls into a deep chasm, landing on a Deku Flower in a large room with the Skull Kid hovering in the distance. It is revealed that the imp-like creature had gotten rid of Epona, and then he proceeds to lay a curse on Link, turning him into a Deku Scrub. The Skull Kid subsequently departs with the darker colored fairy, Tael; however, they accidentally leave behind the lighter colored fairy, Tatl, who apologizes to Link and offers her assistance to help him find a solution to his dilemma. Link and Tatl make their way through a few short rooms that serve as a way to get Link acquainted to his newfound flying abilities as a Deku Scrub.

There is a lonely, withered tree near the exit in the final area of the Catacombs. Tatl brings attention to it, drawing a comparison between its appearance and that of Deku Link. This tree is actually the deceased son of the Deku Butler, and he is seen grieving over it after the defeat of Majora's Mask. The cause of death is unknown, but it has been speculated that his soul was stolen by the Skull Kid and used to transform Link into a Deku Scrub.

Finally, Link walks through a twisted walkway similar to the ones seen in Ocarina of Time's Forest Temple, and enters Termina proper.

Gateway
It is widely believed among fans that Hyrule and Termina exist in two different universes, meaning that Link must have somehow crossed between them to reach Termina. Many of these same fans believe that the Catacombs provided Link with the method to cross over, either upon first falling into them or after passing through the twisted corridor. Alternately, if one assumes Hyrule and Termina exist within the same universe, the Catacombs are likely part of a land bridge linking the two continents.

Trivia

 * The first room, in which Link is cursed, contains two spotlights casting beams of light onto the ground. These show colorful images of shapes, such as stars, circles and squares, for an unknown reason. There are also three triangles shining on the floor that bear a faint resemblance to the crest of the Triforce, albeit with the individual triangles flipped vertically.
 * In the same room, Link lands on a Deku Flower, which can be entered, but has no use.