Development on the Prometheus-class starship project began in the early 2360's at the Beta Antares shipyards. With the Dominion threat becoming more serious, development was stepped up and contruction began in the early 2370's. The Prometheus design borrows its shape from the Intrepid-class starships, except it features four standard warp nacelles similar in design to the nacelles used in the Sovereign-class starship. In 2374, the U.S.S. Prometheus NX-59650 was launched and began top secret field tests.

The Prometheus-class starship was designed for deep space tactical assignments. Its advanced armament also make it a formidable warship. It incorporates regenerative shielding and ablative hull armor. It includes the new Type-XII phasers and Mark-X quantum torpedoes in addition to photon torpedoes and Tricobalt explosives. The Prometheus features a new Multi-Vector Assault Mode. During MVA Mode, the starship separates into three separate ships. The command section containing the main bridge controls the other two sections allowing the ship a distinct tactical advantage over any enemies. After combat situation, the ship can reintegrate into a single vessel.

The Prometheus features four standard warp nacelles and one "mini-nacelle." When separated during MVA Mode, the larger "bottom" and "middle" sections each receive two nacelles. The command module containing the main bridge is also warp-capable. When the ship separates, a "mini-nacelle" on top of the command module is raised. The Prometheus utilizes a new, more efficient warp design that allows it to safely travel at warp speeds without damaging subspace. The Prometheus is the fastest starship in the Federation fleet, capable of sustaining a cruise velocity of warp factor 9.9. It also features the bio-circuitry and gel packs developed and refined in the Intrepid-class starships.

The Prometheus is also the testbed for the new prototype Emergency Medical Hologram Program Mark-II.

In 2374, during the Prometheus field testing, the ship was comandeered by Romulans, led by Romulan Commander Rekar. The Prometheus crew was killed and the Romulans attempted to deliver the vessel to the Tal Shiar, Romulan intelligence. The EMH from the starship U.S.S. Voyager NCC-74656 was transferred to the Prometheus via an alien subspace array in an attempt to communicate with Starfleet. The EMH activated the Prometheus EMH Mark-II prototype and the two holograms worked together to stop the Romulans.