The Crystal Caves is a dark transition level. This area is unique to others because there are no enemies that fire bullets and most of the area will be filled with fast-moving Crystal Spiders. Apart from the enemies, this area also has spider eggs which, when destroyed, can either drop a pickup, weapon, or a lost Alligator. Floor tiles are covered randomly with spiderwebs that slow down your movement.
The Crystal Caves leads to the Frozen City.
- The main theme to the Crystal Caves is "Crystallized Fear". It has no alternate theme.
- The boss theme for Hyper Crystal is "Mind Killer".