In the year 2409, the ship was part of the Starfleet force assigned to protect Starbase 24 from an attacking Klingon fleet. When the starbase was evacuated, a number of scientists from the base were transferred to the McCoy for safe transport out of the system. (STO - "Klingon War" mission: "Starbase 24 (STO)") In the same year, the McCoy was succeeded in name by the USS McCoy, a much larger Destiny-class deep space science vessel. (STO - "Klingon War" mission: "Starbase 24 (STO)")
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