The near destruction of Earth by SHODAN sends shockwaves throughout the world. The events on Citadel station lead to a general rebellion against the government by a mega-conglomerate. TriOptimum, the corporation that created SHODAN falls nearly into ruin. The Unified National Nominate (The UNN), a paramilitary Junta, steps in to fill the power vacuum.

Thirty five years later, Nobel Laureate Marie Delacroix, working under a grant from the dwindling resources of the skeletal TriOptimum corporation, publishes preliminary research findings on a faster than light mechanism. Hungry to get their hands on this technology, the UNN allows TriOp to develop a prototype. The unit performs successfully and work begins on the first FTL starship, the "Von Braun."

The UNN will not allow TriOp to undertake a mission, however, unless an element of the military is attached. To that end, the UNN "Rickenbacker", a heavy destroyer, is literally tethered to the Von Braun. The mission is launched in early 2114.

A few months into its historical journey, the situation is deteriorating. Tension is growing between the civilian elements of the Von Braun and their military counterparts on the Rickenbacker. Things are almost coming to a head when something remarkable happens: The ship receives a distress beacon from the surface of Canopus 5, hundreds of millions of miles outside of colonized space.

A team is sent to investigate the beacon. However, when they return, William Bedford Diego, Captain of the Rickenbacker (and son of Edward Diego) orders an entire deck of the Von Braun cleared of all personnel.

A week later, the players awake from cryogenic sleep to discover that they've been implanted with military grade cybernetic implants. The surgery has destroyed their memory of recent events…They remember neither going in for the surgery, nor what has happened since. They soon realize, however, that something terrible has happened aboard the Von Braun.. They find guidance in both the helpful voice of a surviving crewmember and the logs and emails from those who were not so lucky.

Shadows envelop the decks of the Von Braun, and strange shapes lurk in the darkness. The ships' defenses act as executioner to their former masters for the crime of humanity. And behind it all is the cold voice of a virtual nightmare thought long dead….

SHODAN, the same computer from System Shock 1 will have a strong presence in the game. How she survived Citadel, and what she’s up to this time around is something that you must play the game to find out. Up front, the key villain in this game appears to be "The Many" (note the classic sci-fi name), a race of worm-like creatures that form a collective sentient consciousness. This is sort of like a cross between the Zerg (StarCraft) and the Borg (Star Trek).

It seems that SHODAN, who controls all things robotic & cybernetic, and The Many, who control all things organic, are at war. When they entered the ships, they immediately cannibalized the crews into their armies of mutants & cyborgs.

There is also Xerxes, the computer aboard the Von Braun, who serves an unknown purpose. Dr. Polito is the only other human, as far as we know, who is still alive on the ships, and seems to be your only ally. She will communicate with you over a com-link, giving you vital instructions. The communications will be one-way only.

The story will unfold via emails from SHODAN, The Many, and Polito, logs from the dead crew, and flashback-like visions called "apparitions," where the player uses a piece of hardware known as a Psi-Amp to view events that have happened in the near-past in certain places.

All ‘cut-scenes’ (aside from the intro & endgame) will be rendered in the game engine.

Solitude is something the SS2 developers felt was very important to the success of SS1, so you can expect more of the same in that depertment.

System Shock 2 is not mission-based. It has an overarching storyline broken down into organic "chapters" that often overlap each other. The game will have an overarching storyline, but sub-missions will organically appear throughout the game. Some threads will block other avenues of gameplay (for instance, a key to a door that must be passed to proceed further in the game) and some threads are presented simultaneously ("repair a shuttle" and "reboot the security network") with each thread leading to its own portion of gameplay. This allows us to allow a player who is stuck in one aspect of exploration to proceed in others (an analog version of multiple mission choices). The game is made to be as non-linear as possible, with many, many different ways to solve each problem, and though there is only one ending, there are almost infinite ways of getting there.