Star Trek: Legacy begins a few years after the end of the TV series Star Trek: Enterprise. Starfleet is growing fast and new technologies have been introduced like the tractor beam and starbases. The player takes the helm of the starship Enterprise NX-01 which has been heavily upgraded with all the cutting edge technology and their mission is to find a missing Vulcan ship. During the campaign which unravels over this arc, the player gets the chance to play all the main ships from the five series and films released by that time, all the way to the USS Voyager and USS Enterprise-E. All five captains (Archer, Kirk, Picard, Sisko, Janeway) are voiced by their respective actors from the TV series. Mission objectives vary from combat, through escorting medical ships to their destinatinos to defending planets against incoming asteroids.

The player controls the ship either directly with the keyboard/gamepad or by giving orders to the helm on a map of the current sector or by marking planets or enemies in directly on the screen. Depending on how well a mission is completed, the player can earn command points with which they can buy up to 4 ships, which function like a squad. They can either be given individual commands like defending a position, or switched to back and forth and commanded directly at any time.

During the campaign, the player controls over ships of the United Federation of Planets and fights against Klingons, Romulans and the Borg. In skirmish and multiplayer, all 4 races are playable.