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In 2374, the Cortéz was part of the fleet that took part in Operation Return. Prior to the battle the crew had problems stabilizing the ship's guidance thrusters on the Cortéz' port nacelle. Captain Benjamin Sisko ordered the ship to fall back to make repairs while the USS Sarek moved up to take its position. (DS9: "Favor the Bold")
The Cortéz survived the battle and signaled the USS Defiant that the Dominion fleet had broken off from the engagement and was in retreat. The Cortéz was ordered, along with the rest of the fleet, to rendezvous at Deep Space 9. (DS9: "Sacrifice of Angels")
Later that year, the Cortéz was assigned to patrol the Cardassian border where she went missing. Despite six hours of search by the Defiant they were unable to find any sign of the Cortéz or the 400 crew. (DS9: "Far Beyond the Stars")