The original appearance of Big Five's bad boy alien, the Flagship, was in the game Super Nova.
The Flagship was the most deadly alien ship in Super Nova. Its characteristics included a heartless rotating "eye" and a deadly (although not always accurate) lightning-like laser bolt that the Flagship could fire at your ship from any point on the screen. The ominous nature of the Flagship was reflected by its 2,000 point scoring value - making it the highest value target in Super Nova.
A similar version of the Flagship appeared in the game Cosmic Fighter. There the Flagship was worth a varying number of points, up to around 900.