"Flag captain" was a term used to refer to the commanding officer of an admiral's flagship. The flag captain had authority to take command in the event the admiral was incapacitated.

During the 2409 Klingon Defense Force raid on Utopia Planitia, Lieutenant Commander Brokosh served as flag captain to General K'Bor aboard IKS mupwI'. (Bait and Switch: Red Fire, Red Planet)

Captain Bronok Zell served as flag captain to Admiral Amnell Kree aboard USS Marduk. (Template:Foundry; Bait and Switch: Bait and Switch)

In 2410, Captain Kanril Eleya briefly served as flag captain to Rear Admiral Eviku nd'Ashalef, but offloaded him and his staff to USS Dominant when it became clear that the portal to the mirror universe in the Arawath system would only allow USS Bajor to pass. (Bait and Switch: The Wrong Reflection)

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