The player takes the role of human Cadet David Forester, leader of a cadet group at Starfleet's San Francisco–based Command College. The player has to pass all the simulated missions, optionally including the infamous Kobayashi Maru scenario. The scenarios, in addition to simple combat situations, include a recreation of Kirk's near-disastrous starship confrontation with Khan Noonien Singh which Kirk ruefully admits is used to teach cadets to avoid his serious mistake that nearly doomed his ship. In addition, between simulator scenarios, Forester must keep his crew in check and prevent personality clashes from lowering team performance by choosing the right dialogue options during cutscenes.

The cadet crew consists of a Vulcan science officer called Sturek, a female Andorian communications officer named Vanda M'Giia, and a detached and shy human engineer Robin Brady, with Trill Jana Akton at the helm and human Geoff Corin at navigation.

During the course of the game it is possible to foil the machinations of the Vanguard — a fanatical terrorist group dedicated to overthrowing the Federation government and installing Kirk as a despot — and to investigate the cause of increasing tensions around the Klingon Neutral Zone. On the other hand, it is possible to be dismissed from the Academy in disgrace if the wrong choice is made during certain full motion video sequences.