Game play consists of the player starting out on the bridge of the Enterprise-D, from which the player receives orders and other messages on the viewscreen. From here, the player can also access the conn and set course to any of a large list of planets. If the need arises, the player can also access the tactical station, from which one controls the Enterprise in battle. The player can also access the turbolift, which takes one to the transporter room. Unless the planet the player chooses is a part of a mission, the player will not be able to leave the bridge.

If access to the transporter room is allowed, the player will then be able to choose members of an away team to beam down to the planet to carry out a mission. The player then takes control of the away team once they are on the planet. One member of the away team will lead while the others follow. The player can alternate between each of the four away team members.

Among the characters the player is able to choose for away team missions are Jean-Luc Picard, William T. Riker, Deanna Troi, Worf, Beverly Crusher, Geordi La Forge, and Data. The player can also choose from several non-senior staff members, all of which were created for the game (and whose features are based on those of the game's designers). Each crewmember is armed with equipment to match their specialties. For example, Picard, Riker, Data, La Forge, and Worf all carry phasers because of their high tactical abilities, while only Data and La Forge carry a tricorder because of their high technical abilities. Medical officers, such as Dr. Crusher, carry a medical tricorder in order to heal injured members of the away team. All senior officers carry a command insignia, which allows them to lead the other members of the away team. All characters has various levels of stamina as well, which also comes into play in choosing an away team. For example, Worf being a Klingon has a much higher stamina rating than La Forge or Dr. Crusher. La Forge's VISOR also allows him to see in the dark. Data is the most invaluable away team member as he is able to carry a phaser, a tricorder, and a command insignia. His android body also gives him an exceptionally high stamina rating which makes him extremely durable against damage as well as environmental hazards. His positronic brain also allows him to see in the dark, although, not as well as La Forge (a reference to TNG: "Encounter at Farpoint" when Data tells Riker he cannot see as well as La Forge).

During an away mission, the player must take great care not to lead any senior staff members into harm's way. Although no senior staff members are killed (only the crewmembers designed for the game die; others are transported to sickbay), too many casualties will result in the Enterprise aborting the mission (effectively ending the game). When a senior officer's health is depleted, the away team will be forced to return to the Enterprise and the player must begin the level again. Should any senior officer other than the captain be injured three times, the Enterprise will abort the mission altogether and the game will be over. Should Captain Picard sustain severe injury once during a mission, the entire game will be over immediately.

The final part of the gameplay is the space battle, which is controlled from the tactical station. In this scenario, the player has an overhead view of the Enterprise and the enemy vessel. During battle, the player controls the movements of the Enterprise, as well as the firing of the ship's photon torpedoes and phaser arrays. Naturally, the scenario ends when either the enemy vessel or the Enterprise is destroyed; if damaged enough, some enemy vessels will offer a surrender, and the player may also open hailing frequencies in the hopes the enemy will leave them be.