If you fail to exit a level after a certain amount of time, the Flagship will appear next to the door that you used to enter the level.
The Flagship will move steadily and continuously toward you. Shooting it has no effect. The Flagship can move through walls and will destroy any robots it runs into. If the Flagship touches your character, you lose a life.
As it moves at the same speed as your character, your only escape from the Flagship is to move your character to an exit before it gets to you.