Zaxxon's Motherbase 2000 is a sci-fi shooter exclusive to the Sega 32X console, built around the gameplay formula of Sega's arcade classic Zaxxon . The game features a diagonally scrolling playfield, creating a pseudo 3D environment. The backgrounds are drawn using 2D scrolling planes, but the enemy and ship objects are drawn using 3D flat-shaded polygons.
The objective of each level is to eliminate all enemies without being targeted yourself, adding a layer of strategy to the game. However, the basic spacecraft has limited firepower and can only withstand one hit, making survival even more challenging. With few power-ups available, players must jump onto enemy ships to take control of their weapons systems, unlocking a variety of player-controllable vessels.