Ysanne, who works for the Federation Police and pilots the space ship Relentless, is a tough feminist/misandrist redhead, while Jack is a notorious thief and womanizer.

The locations and evolving plot are largely the same both ways, but the player can experience two sides of the story, and will be solving different puzzles.

After being jailed aboard the Relentless, Jack escapes his cell and destroys the ship's hyperdrive, when Ysanne is notified about a disaster on Lixa, a mining planet in the Altaros Nebula sector.

Jack must steal back the Gyro Mechanism taken from their ship, while Ysanne tries to save the lives of soldiers who are being sacrificed needlessly.

When this task is complete, the protagonists receive a distress call from Lowe's Planet where they must save the colonists from an assault by an indigenous species.

In that planet, the player will meet Nalm N'Palm, his sidekick from the previous game, who has joined the Interstellar Xenophobic Mercenary Force.