The players take the role of Starfleet cadets. The cadets are asked to participate in a U.S.S Enterprise-D simulation. Taking the place of Captain Jean-Luc Picard, they must embark on a series of mission-based goals and perform many tasks (in the form of mini-games) such as diverting power to shields, Transporter Systems, Navigation, Tactical, and more.

As the player successfully completes missions, they gain rank. Starting the game as an Ensign, the player can be promoted to Lieutenant, Lt. commander, Commander, and finally Captain. Each rank has a specific password the player can input to resume the game at whatever rank the player had previously achieved. Combat missions involve fighting enemies of varying strengths and numbers, with Talarians being the weakest and renegade Klingons being the most difficult (except for the Borg, who only appear in one mission).

Before each mission, Captain Picard gives the player a mission, ranging from transporting ambassadors from one planet to another, to destroying Ferengi pirates, to (eventually) destroying a Borg cube.