This page is a room-by-room breakdown of Hidden Desert. All "recurring features" of a given room — namely, enemies that respawn whenever the room is reentered and blue chests that self-refill whenever the zone is exited and reentered — are listed in bold above one-time collectibles and events. All chest icons shown in the map screen below are the zone's blue chests.
- Screen 1:
- ×1 Amy, ×2 Poison Toad
- Exit to Forbidden Underground Waterway
- Screen 2:
- ×2 Amy, ×1 Living Fossil
- Sink into sand to drop into Screen 3
- Screen 3:
- ×1 Living Fossil
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Screen 4:
- ×1 Allocer
- ×2 Amy (Hard)
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Screen 5:
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Breakable wall containing Capacity upgrade
- Screen 6:
- ×1 Allocer
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material) (requires Reflector Ray/Double Jump)
- Screen 7:
- Screen 8:
- ×3 Allocer, ×1 Vul'sha
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Screen 9:
- ×1 Zepar, ×1 Allocer, ×1 Vul'sha, ×1 Poison Toad
- Screen 10:
- ×2 Amy, ×2 Allocer, ×2 Poison Toad, ×1 Vul'sha
- ×2 Amy (Hard)
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Screen 11:
- ×1 Zepar
- Bookcase about Lasting Wound technique
- Screen 12:
- Screen 13:
- Screen 14:
- ×1 Water Leaper
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Portal to The Tunnels (opens only after reaching Den of Behemoths)
- Screen 15:
- Alfred (boss)
- Screen 16:
- Deep Sinker shard on stand (requires defeating Alfred)
- Screen 17:
- ×1 Amy, ×1 Allocer, ×2 Poison Toad, ×1 Vul'sha
- ×1 Amy, ×1 Vul'sha (Hard)
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- MP Max Up
- Screen 18:
- ×2 Allocer, ×2 Vul'sha
- ×1 Allocer (Hard)
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Screen 19:
- ×1 Zepar
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Screen 20:
- ×2 Amy (Hard)
- Exit to Screen 28 (normally requires Invert or High Jump, but can also be reached by jumping at the end of an upward Reflector Ray)
- Screen 21:
- ×1 Amy, ×1 Allocer, ×1 Vul'sha
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Screen 22:
- ×2 Allocer, ×1 Rocky
- ×2 Amy (Hard)
- Blue chest containing Mithridate, Mahogany, Crystal, and Gold (material)
- Breakable wall leading to Screen 23
- Screen 23:
- ×1 Zepar
- Green chest containing Traveler's Hat
- Screen 24:
- Screen 25:
- ×1 Vul'sha (Hard)
- Green chest containing Weighted Ring
- Screen 26:
- ×1 Living Fossil
- Breakable wall containing MP Max Up
- Screen 27:
- ×1 Amy
- ×1 Allocer (Hard)
- Exit to Forbidden Underground Waterway
- Screen 28:
- HP Max Up
- Green chest containing Potent Ammunition/R