Crystal Mine is a mine located inside a hollowed-out crater. The sky is as well dark and polluted here. The mine itself is connected to Robotropolis via a railway line, which Swat-Bots use to transport Worker-Bots to their workplaces in the mines. The railway station is located in the Crystal Mine's crater, and has a lift that leads down to the lower levels of the mine.
Dr. Robotnik's forces have drilled a hole in the crater, down to the mines below. It is through this hole that very large objects, such as massive Energy Crystals, can be extracted from the Crystal Mine. Underneath the crater is the main sector of the mine. This sector possesses a main building that controls the work in the mine, as well as a large crane to pull out large Energy Crystals.
The Knothole Freedom Fighters came to the Crystal Mine by train in pursuit of Chuck after escaping the Swat-Bots from Robotropolis. Before entering the mine, Sonic and Bunnie caught Chuck. The heroes then gave him a Power Ring, temporarily restoring his free will. Chuck proceeded to lead the Knothole Freedom Fighters down to the lower parts of the Crystal Mine where he showed them that Dr. Robotnik's forces were ready to extract a giant Energy Crystal, whose removal would destroy Mobius's eco-system. The Knothole Freedom Fighters decided therefore to stop its extraction. While Sally, Antoine and Rotor went on to sabotage the crane extracting the Energy Crystal, Sonic, Chuck and Bunnie took control of the mine's Dinobot. During their mission, Sally, Rotor and Antoine managed to turn off the robot working on the crane, but they failed to deactivate said crane. As such, Sonic, Chuck and Bunnie used the Dinobot to destroy the ropes hoisting the Energy Crystal out of the mine, causing the Energy Crystal to fall back into the mine and shatter upon impact. The heroes then evacuated back to the surface. However, they had to leave Chuck behind there when he began to lose his free will to Robotnik's programming. The heroes proceeded to escape from the Crystal Mine by train, allowing them flee from the Swat-Bots pursuing them.
Snively later contacted the Swat-Bots in the Crystal Mine, whom Dr. Robotnik ordered to use the Mind Probe on a roboticized dragon to interrogate it. Thanks to this, Robotnik were reminded of Dragon's Nest.