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Initially the ship was under the command of Raakin until the rest of the Augments rebelled against him, after choosing to follow Malik, who would continue to command the vessel. Soonafter the Augments received a signal from their father, Arik Soong, and set course to intercept Enterprise, on which Soong was being held.
When they reached Enterprise, the ship was under attack by two Orion Interceptors. The Bird-of-Prey quickly destroyed one of the interceptors and the other retreated. After taking aboard Soong from Enterprise, they departed for Cold Station 12 where the Bird-of-Prey remained above the facility with a skeleton crew. They engaged Enterprise in hit and run tactics and after the crew returned, they set course for the Briar Patch. However, Malik and his followers rebelled against Soong and his pacifist ideals. Soong escaped in an escape pod with the help of Persis, and later went on to help Enterprise destroy the Bird-of-Prey and all of the Augments with it. (ENT: "Borderland", "Cold Station 12", "The Augments")