The Battles against the Borg at Wolf 359 and Sector 001 both showcased several flaws in Starfleet battle readiness and threat response capabilities. One of the main concerns in the eyes of Starfleet Command was that early on in both battles, the Admiral's flagship in command of the fleets was destroyed, leaving the remaining forces uncoordinated and with a crippled chain of command.

Cerberus was built specifically to try and offer a solution to this problem. The ship was not intended to separate into three independent crafts during battle as other Prometheus-class vessels, but rather to function as a resilient flagship able to withstand heavy barrages of enemy fire and still coordinate fleet movements effectively.

The redundancy inherent of the class design, with its 4 main warp nacelles, 3 independent computer cores, 6 impulse engines, and many other redundant systems, made it a perfect candidate for this role. The ship still retained the ability to separate in an emergency, but its spaceframe was heavily modified to prioritize total hull strength when the ship was connected together, unlike other Prometheus-class ships.

Originally intended to enter service in 2375, delays with the spaceframe modifications pushed the commissioning of Cerberus to 2376, just enough to miss the end of the Dominion War. The vessel became the new flagship for Rear Admiral Ross, and while it didn't see the heavy fighting it was designed to withstand, still proved a successful and versatile peacetime flagship for the Admiral, showing the flag in many diplomatic missions during the post-war reconstruction of the Alpha Quadrant.

• Cerberus was mentioned as the post-war flagship for Admiral Ross in several Star Trek novels. The registry number came from the RPG sourcebook "Star Trek Adventures: Utopia Planitia".