(written from a Production point of view)
The following year, a sequel was released, Star Trek: Starfleet Command II - Empires at War. This release was popular enough that an expansion pack was released in 2001 for it, Star Trek: Starfleet Command - Orion Pirates. This expansion pack was one of the final Star Trek game releases by Interplay.
Activision took over the franchise, releasing Star Trek: Starfleet Command III in 2002. This third, and final, game in the series was set immediately before the events of Star Trek Nemesis and dealt with a conflict between the newly strengthened Klingon/Federation Alliance and the Romulan Empire.
Unfortunately, Activision and Paramount became embroiled in a legal battle during this period, and the release of the game ended up being limited due to the dispute.