The Flagship refers to the Precursor vessel flown by The Captain in Star Control II. It is also known as the Vindicator, the default name on the 3DO version of Star Control II, though the name can be changed during the game. The name SIS (an abbreviation for Super Integrated Starship) is also sometimes used; it is how the ship is refered to internally in the code, but never in the actual game or manuals.
The ship proper is a framework created by the automated Precursor base on Unzervalt. Separate Modules can be attached to it. The modules have varying effects from increasing the ship's manuverability and speed to storing crew and other supplies. The ship can also be fitted with a host of weapons and energy systems as well as having docking space for up to 12 other smaller ships.
This ship becomes the flagship of the New Alliance of Free Stars and is integral in that group's completion of its ultimate objective. Sadly, it had to be sacrificed to destroy the Sa-Matra and end the Second War, by way of the Chmmr attaching the Utwig Bomb and a number of their own enhancement devices to the ship's hull and energy generation systems.
See also: Mark II