System Shock 2 begins with the protagonist awakening from cryogenic sleep aboard the Von Braun spaceship. He discovers that during his nap, cybernetically implants were implanted into his body. The unpleasant surprises don't end there. Most of the spaceship's inhabitants are killed, and the survivors are turned into aggressive mutants. Everywhere a mysterious race of parasitic organisms is rampaging, fought against by an out-of-control artificial intelligence. The protagonist is not happy with either side of the conflict.

After training, the System Shock 2 hero is allowed to choose one of 3 classes:

• Marine. He is proficient in any type of weapon, strong and resilient, but does not have any particularly outstanding abilities.
• Hacker. A master of hacking, capable of extracting additional resources from equipment, as well as winning over the ship’s mechanisms to his side.
• Psionic. An analogue of a fantasy magician, using special energy coupled with implants to distort the reality around him.

The gameplay of the game remains a first-person action RPG. The protagonist wanders through the open corridors of the Von Braun and Rickenbacker ships, fights opponents using any available means, collects items and upgrades. Along the way, he completes story missions. Despite choosing a class at the beginning, the character is allowed to be upgraded without restrictions. And the path to achieving goals is chosen by the player himself, the path is mainly traversal and linear.