Apart from live-action cutscenes with branching dialogue that decides the course of the cutscene (allowing for the player to even risk summary dishonorable discharge in some circumstances), Starfleet Academy is a 3D space flight simulator, allowing players to command Federation starships of various classes in the single-player campaign, including the iconic Constitution-class - the ship class which includes the USS Enterprise - as well as its successor, the USS Excelsior. Ships are controlled through keyboard shortcut commands, though a joystick may also be configured. The mouse is usually used to interact with the ship's sections when off-action, which include the science station, communications, engineering, and even a database library with most persisting elements of the Star Trek universe.
The objectives of most Starfleet Academy missions are to warp to a target system, destroy or capture enemy starships or installations by disabling them or protect allied targets, and return to a home base. Elements of diplomacy through communications are often featured in these missions. As one plays through the game, progressively stronger enemy forces do appear that require the player to use extensive maneuverability and have total familiarization of the ship's resources, especially damage control and power allocations. While some missions do have allied vessels, the player cannot control them directly, nor enemy vessels can be boarded and taken over, unlike the sequel Star Trek: Klingon Academy.
All starships have shields and a variety of combat systems, including weapons, tractor beams and ECM. Shields are divided into six faces, one for each fore, aft, port, starboard, dorsal and ventral side of the ship, and must be battered down before significant damage can be inflicted to the ship's hull or subsystems.
In addition to simple combat situations, some missions include more complex scenarios such as a re-creation of the near-disastrous starship confrontation with Khan Noonien Singh as well as the Kobayashi Maru scenario, both depicted in Star Trek II: The Wrath of Khan, as well as a recreation of the episode "Balance of Terror", from the original series. Other scenarios have an overarching plot around them, such as a star system whose sun faces an imminent supernova due to the continuous draining by a space faring creature, a governor of the Klingon Empire acting illegally against the Federation with the aid of pirates and Romulans, and a once peaceful alien species turned hostile by a psychic that formed a cult of personality.