The Crystal Caves is a dark transition level. This area is unique to others because there are no enemies unique to the area 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".