In late 2369, Vice Admiral Nechayev mobilized a fleet consisting of the Agamemnon and fourteen other ships with the stated aim of patrolling and defending Federation colonies from an anticipated second Borg invasion. The ships were divided into five task forces with the USS Gorkon as the flagship. Agamemnon was assigned to task force three under the command of Captain Jean-Luc Picard. For the duration of the task force's existence, the Agamemnon would serve alongside the USS Crazy Horse and the USS Enterprise-D. (TNG: "Descent")
USS Agamemnon was one of the possible names for the Federation battleship in the PC game, Star Trek: Starfleet Command.
In the Lost Era novel Serpents Among the Ruins, a USS Agamemnon, whose captain and first officer were Esteban Rodriguez and "Iron Mike" Paris (father of Owen, grandfather of Tom) was a casualty of the Tomed Incident – though in reality, the ship, and all other Starfleet installations lost in the catastrophe – was empty, rigged to emit false life signs, members of its "crew" killed in action in the past year and their death covered up by Starfleet until then.