At the start of the level, one or more Flagships are outside of the grid. The Flagships occasionally fire laser bolts that have a transformative effect. These shots turn Ramships into Flagships or a clone of your ship.
Once all Ramships have been cleared from a level, all Flagships enter the grid and periodically fire laser bolts at your ship. These laser bolts can be fired at your ship from any point on the screen. Your ship is destroyed if hit by a laser bolt or if it runs into a Flagship.
All of these Flagships must be destroyed in order to exit the level. You receive a variable number of points for destroying a Flagship (from around 200 to 400), with the exact amount being displayed on-screen after the Flagship is shot.