Here's the plot:
The story begins in 2114, forty-two years after the events of System Shock. After joining the United National Nominate, the protagonist ó Soldier G65434-2 ó is assigned to the Rickenbacker, a military spacecraft. The Rickenbacker is escorting the Von Braun, an experimental faster-than-light starship, on its maiden voyage. A few months into the journey, the ships respond to a distress signal from the planet Tau Ceti V. A rescue team is sent to the planet surface where they discover strange eggs. The eggs infect the rescue team and integrate them into an alien communion that calls itself the Many. The infestation eventually overtakes both ships.
The soldier awakens in a cryo-tube on the medical deck of the Von Braun with amnesia due to a computer malfunction. He is immediately contacted by another survivor, Dr. Janice Polito, who guides him to safety before the cabin depressurizes and demands he rendezvous with her on deck 4. Along the way, the soldier battles the infected crew members. The Many also telepathically communicate with him, attempting to persuade the soldier to join their collective.
After restarting the ship's engine core and purging an elevator shaft, the soldier reaches deck 4 and discovers Polito is dead. He is then confronted by SHODAN, a malevolent artificial intelligence that devastated Citadel Station, a fictional space station, in the previous game. It is revealed she has been posing as Polito to gain the soldier's trust and is responsible for creating the Many. They are the results of her bioengineering experiments on Citadel Station. The hacker (System Shock 1) ejected the grove that contained her experiments to prevent them contaminating Earth, an act that also allowed part of SHODAN to survive the events of the first game. The grove crash-landed on Tau Ceti V. While SHODAN went into forced hibernation, The Many evolved beyond her control. SHODAN issues an ultimatum to the soldier, stating his only chance for survival lies in helping destroy her rebellious creations.
Efforts to regain control of the main computer fail. SHODAN informs the soldier that destroying the Von Braun is their only option, but he must transmit her program to the Rickenbacker first. While en route, the soldier briefly encounters two survivors, Tommy Suarez and Rebecca Siddons, who flee the ship aboard an escape pod.
With the transfer complete, the soldier travels to the Rickenbacker and learns both ships have been enveloped by the infection's source, a gigantic mass of bio-organic tissue. The soldier enters the biomass and destroys its core, stopping the alien infection. SHODAN congratulates the protagonist and informs him of her intentions to merge real space and cyberspace by subverting the reality-altering mechanics of the Von Braun's faster-than-light drive. The soldier confronts SHODAN in cyberspace and defeats her. The final scene shows Tommy and Rebecca receiving a message from the Von Braun. Tommy responds, saying they will return but Rebecca is feeling ill. She is shown speaking similarly to SHODAN.
and that's about it.
