In Carrier Command: Gaea Mission, players manage an armed vehicle carrier while navigating a vast open archipelago, combining real-time strategy with action elements. Players must establish island bases, gather resources, and engage in tactical combat against enemy forces.

The storyline follows Lt. Myrik, a member of the United Earth Coalition, as he embarks on a mission to restore Earth's water supply by conquering the Dead Zone on the moon Taurus, following a catastrophic war that has devastated the planet.

Carrier Command: Gaea Mission stands out with its unique blend of strategic planning and direct combat control, allowing players to seamlessly switch between managing their carrier and engaging in real-time battles, enhanced by a Picture-in-Picture interface.