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A flagship is a particular ship in a fleet or task force that carries the "flag officer", the officer who has command of the entire fleet. This is usually, but not always, the largest and most powerful ship in the fleet.

Flagships in Star Trek

In TNG, the USS Enterprise is repeatedly described as the "Federation flagship", even when it is not operating as part of a fleet. This indicates that Starfleet uses the term to mean "the best/most prestigious ship in our entire fleet" rather than the command ship of a specific fleet or task force.

Flagships other than the Enterprise

Flagships in Stargate