Step into the boots of a Starfleet officer taking command for the first time -- in the sink-or-swim circumstances of a disaster in deep space. A sun erupts unexpectedly, damaging the player's ship and killing the captain. As the next ranking officer, the player takes the command chair and the mission of discovering the cause of the deadly blast. Through investigation of the strange stellar explosion, the fledgling captain is drawn into an epic plot involving the Cardassians, the Klingons, and perhaps even the Romulans. Forces behind this unexplained "accident" may threaten the foundations of the Federation itself.

The game offers a first-person perspective from the captain's chair for a useful view of the 3D bridge and its officers. As in the television shows and movies, the bridge crew is well trained to report pertinent information and await orders. Star Trek: Bridge Commander is designed for compatibility with many contemporary voice-control peripherals, allowing the hardware-equipped player to issue commands by speaking them. The game's story was developed with the help of D.C. Fontana, who wrote four episodes of Star Trek: The Next Generation and served as an associate producer for the series.