Ian Recker, a spy for Earth, is sent undercover as a prisoner so that he can become enlisted in the Krill army. He is suited up with a parasitic suit of armor that gives him enhanced strength and the ability to merge with Krill ships, which are living organisms. However, he soon discovers that all is not as it seems in this war, and Recker must decide which side he is fighting for.
Sigma Star Saga is a hybrid of the side-scrolling shooter and RPG genres. Players interact with characters and explore the overworld, and are frequently 'summoned' by random ships for battles. To successfully complete a battle, the player must defeat a preset amount of enemies, and they gain experience with each enemy defeated. As players explore the overworld, they can also discover Gun Data, which can be used to customize the player's shot with over 15,000 different weapon combinations using abilities such as rapid fire, vertical shot, and experience gain.