In a maritime fleet, the ship occupied by the fleets commander (usually an admiral); it denotes this by flying his flag
The vessel which carries the commanding officer of a fleet or squadron and flies his distinctive flag or pennant
The flagship of a group of things that are owned or produced by a particular organization is the most important one. The company plans to open a flagship store in New York this month
A flagship is the most important ship in a fleet of ships, especially the one on which the commander of the fleet is sailing