The Secret Base is a stage that made its debut in the original Vigilante 8. Inspired by a popular area known as Area 51, Secret Base is a stage that parodies what conspiracy theorists believe to be located within the confines of the restricted area. The stage is complete with aircraft hangars, satellites, fighter jets, a water tower and a large building which can be deduced as the main headquarters. Hazards in the area include laser cannons, which fire at the player when nearing a prohibited, yet accessible, area.
- If the player shoots off the security ladder holding the fighter jets in place, the jets will proceed to take off on the runway on their own.
- Located in an undisclosed location in the stage is a prohibited area guarded by laser towers. Avoiding the lasers, the player can easily shoot down the gate guarding access to this area, in which the player can find an assortment of buildings containing Special Weapon Crates, Wrenches and Power-Ups.
- Inside one of the hangars beside the runway, there is an alien aircraft (resembling the Luxo Saucer driven by Y the Alien). If the player destroys it, he will be awarded with Power-ups, a Special Weapon Crate and more ammo for one of the standard weapons that he already has.