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In 2381, the Jefferson, along with several civilian cargo ships carrying supplies out to the Velos, who had been cut off from regular supply runs, where attacked. The Jefferson managed to draw most of the fire from the attacking So’jan vessels, but some of the cargo ships were damaged. ("Everything Changes")
In 2382, the Jefferson participated in the Battle of Minark and was damaged. When coming out of at Deep Space Five, the ship's damaged deflector dish malfunctions causing the starship to explode. ("Torment and Woe", "Dawn")