The Deep Sea Hideout was Nefarious's secret base and first base for operations on Aquatos. It was located entirely undersea, and was only accessible via seaworthy spacecraft or specialized tunnels. The base was made up of vast tunnels and waterways, making for a confusing obstacle course, as it was guarded by Dr. Nefarious's best Tyhrranoid guards and robotic security. There were bridges and blast doors only accessible with the use of a Hacker. The base contained Nefarious's office, which held his entire Secret Agent Clank collection and the star map. Illegal weapons dealer Slim Cognito had also set up shop here, apparently on the run from the authorities after a botched weapons sale. Finally, the base leaded into the sewers of Aquatos, possibly the grossest in the galaxy. The Plumber was here looking for Sewer Crystals.
- Ratchet & Clank: Up Your Arsenal (first appearance)