Star Control II: The Ur-Quan Masters

The colonists activated the Precursor machinery and found out that it was programmed to build a starship.

Link to this screenshot:

The Tobermoon, an Earthling ship, discovered an ancient Precursor subterranean installation in a cave on the surface of an uninhabited planet in the Vela star system. The player begins the game as a commander of the Precursor starship, who returns to Earth to find it enslaved by the Ur-Quan. It is discovered that the rest of the humans' allies in the war against the Ur-Quan have either been eradicated, put under a slave shield, or put into service as Ur-Quan battle thralls. As the player progresses, it is revealed that the Ur-Quan are fighting an internecine war with the Kohr-Ah, a subspecies of Ur-Quan who believes in eradicating all life in the galaxy, as opposed to enslaving it.

This game has an incredibly detailed and funny story, a Spacestar-style combat engine and well thought-out spacecraft design. Many conversations and speeches, like that of the lecherous last surviving male of the Shofixti species, are quite funny, and some, like that of the aspiring screenwriter Yehat, are hilarious!