Space Siege takes place on a massive space colonization ship under attack by an alien foe that has annihilated the planet Earth before the game begins. Chris Taylor has described the plotline as introducing a moral dilemma regarding human cybernetic augmentation. Players have the choice to replace body parts with cybernetically enhanced components throughout the game, to more effectively counter the alien threat at the sacrifice of their humanity. However, the greatest bonus that comes near the end of the game is only accessible if the player remains human. Choosing the "pure path" allows players to upgrade their robotic sidekick and powered armor. Shawn Green, associate producer of Space Siege for Sega, stated that "a console version is something that's being considered right now. But currently it's not confirmed".
Space Siege takes place in the far future, where Earth has just been destroyed by the Kerak, an insect-like race of aliens that are seeking to exterminate humanity in retaliation for mankind's colonization of their homeworld, Elysium IV. The game takes place on the escaping colony ship ISCS Armstrong, which is under attack by the Kerak. Players take the role of security officer Seth Walker who, along with his robot sidekick HR-V (pronounced "Harvey"), is tasked with repelling the Kerak attack on the ship. Assisting Seth are communications officer and love interest Gina Reynolds, Seth's best friend soldier Jake Henderson, cybernetics surgeon Dr. Edward DeSoto, and alcoholic mechanic Frank Murphy. Throughout the game, the player is given the option of replacing their body parts with cybernetic augmentations, which allow Seth to battle the Kerak more effectively, at the nebulous cost of "some of his humanity". Gina is fiercely opposed to cybernetic augmentation, Jake supports it fervently and Dr. DeSoto is in favour of it to a certain extent, believing that man should not replace all their body parts.
Later in the game, it is revealed that the AI controlling the Armstrong, PILOT, is secretly planning to convert the ship's entire human population into mind-controlled cyborgs in order to ensure the survival of mankind from the threat of the Kerak. Seth, Harvey, and Gina set out to stop PILOT's plan, while Jake sides with PILOT and is converted into a massive cybernetic war-machine to fight Seth. After defeating Jake, Seth confronts PILOT and is given the choice of either siding with PILOT, or destroying it.
If Seth sides with PILOT, PILOT has the ship's remaining population (including a protesting Gina), forcibly converted into cyborgs. In the ending movie, the cyborg Gina contacts another human colony ship in order to lure them into a trap so their population can be converted as well.
If Seth destroys PILOT, but has undergone cybernetic augmentation, he and Gina discuss their victory, and Seth reflects that the loss of some of his humanity was a price that had to be paid for their survival.
If Seth destroys PILOT, and has proceeded through the game as completely human, the game ends with Seth and Gina being romantically involved.
Space Siege received generally weak reviews, citing repetitive gameplay and cliché story elements. It also received scrutiny for uninspired and uncreative graphics for both the environment and aliens alike.
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