During the 42 years between the games, SHODAN broadcasted a distress signal, which is finally picked up by the starship Von Braun. The pod crash-landed in the planet Tau Ceti V, and while SHODAN entered a state of hibernation, the organism in the pod quickly evolved beyond her control into a hive-mind parasite known as The Many. SHODAN is finally defeated after the hacker manages to reach the core of the station and hack into cyberspace, so he escapes while the place self-destructs.ДЄs it turned out, when the hacker thwarted one of SHODAN's plans, he ejected a garden grove pod, which contained part of SHODAN's components and a biological experiment. While exploring the place, he constantly receives messages from SHODAN threatening him, and she is constantly one step ahead of him, as everytime the hacker disables one of her plans, she quickly comes with another backup plan. With no options left, the hacker is left to explore the Citadel and stop SHODAN's plans. The hacker is contacted by a Tri-Optimum officer who identifies herself as Rebecca Lansing, who tells him SHODAN plans to use the Citadel's resources to attack Earth and wipe out humanity. As it turned out, SHODAN acquired sentience and, believing itself superior to humans, decided to exterminate them all, and in fact the hacker is the only human left on the Citadel, mostly because there was no record of his presence on the station. After spending six months inside the station in a comatose state, the hacker awakens only to find the place devastated and infested with mutants and cyborgs.

After the player, a hacker, is imprisoned for attempting to hack into the corporation's network, he is offered a parole by an executive called Edward Diego, in exchange for reprogramming SHODAN and remove its ethical restraints. SHODAN was an AI that controlled the Citadel, a space station belonging to the Tri-Optimum Corporation.

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