Carrier Command is one of the first real-time strategy games. The player controls an advanced, futuristic aircraft carrier equipped with fighters, amphibious vehicles, laser defenses and a fleet of drones. The mission is to build a series of resource bases, factories and defense structures on the islands of the archipelago. The problem, however, is the existence of a second, even more advanced aircraft carrier under the control of a terrorist organization that has an identical mission.

When moving between the islands, the player must decide what objects to build and where they will best fulfill their task. Resource islands provide materials from which factories can make weapons and vehicles, but can be quickly taken over by the enemy if attacked while the player is away.
While controlling an aircraft carrier, the player can take control of fighters and amphibious vehicles, using them to attack enemy islands and even an enemy aircraft carrier if found. The combat equipment of the vehicles is fully configurable, adapting them to the needs of the mission. The invasion of the island may require the launch of a virus bomb, thanks to which the player will be able to take control of enemy command systems.

The goal of the game is to find and destroy the enemy aircraft carrier, which requires a solid supply infrastructure and a strategy to deplete the enemy's resources.