The dungeon is forty floors in total. Every five levels follows the theme of one of the eight worlds of the Drablands, starting with the Woodlands and following in sequence up to the Sky Realm. Unlike normal stages, the player begins with only one fairy available instead of three, although more can be acquired as they progress. The Great Tripini appears at the entrance and will provide Link information about the Den of Trials.
In the first four levels of each world's "set", the Links must face various enemies from that world in a coliseum-like setting. Some enemies will be "dark" variants of normal enemies, which take more hits to defeat and can inflict curse status with their attacks. Once all enemies in the level are defeated, the exit to the next level will appear. There are no enemies or obstacles in every fifth level, which will instead have three treasure chests, a Squiddy, and a small chest with an extra fairy. Exiting every fifth level will also automatically save.
On the 39th level, the Links will face a trio of Dark Links, each with a different item. The Dark Links' items will be enhanced versions, as though they were under the effects of outfits like the Kokiri Clothes or Big Bomb Outfit. Unlike the normal Links, the Dark Links do not share a life meter, and each one must be defeated. The 40th level has eight treasure chests instead of three, and the first time the player clears the Den of Trials, they will also obtain the Fierce Deity Armor.
| Link · Princess Styla · King Tuft · Madam Couture|
—Full list of characters
|Arrghus · Blizzagia · Margoma · Moldorm|
| Hytopia · Woodlands · Riverside · Volcano · Ice Cavern · Fortress|
—Full list of locations
|Gripshot · Bomb · Boomerang · Bow · Fire Glove · Gust Jar · Hammer · Water Rod|