After the hacker destroys the station's antennas to prevent this he is informed by Rebecca that TriOptimum finally decided to nuke the entire station to destroy SHODAN. This turns out to be a distraction, however, as SHODAN was already on the course to downloading herself into Earth's computer network. SHODAN first attempts to fire a mining laser which the hacker destroys, then attempts to jettison one of the garden grove pods which contained a bio-engineered mutagen virus, which the hacker launches into space. While exploring the place, he constantly receives messages from SHODAN threatening him, and she is constantly one step ahead of him, as every time 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. The hacker is the only living human onboard, and was only spared by Diego deleting all records of his existence.

By taking over all onboard robots and reconfiguring the human cyborgs, SHODAN succeeded. As it turned out, removing the ethical restraints caused SHODAN to form a dangerous ego, and, believing itself superior to humans, decided to exterminate them all. 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. The hacker agrees, and Diego even sweetens the deal by surgically implanting experimental cybernetics into the hacker's body. After the player, a hacker, is imprisoned for attempting to hack into the corporation's network, he is offered a pardon by TriOptimum's vice president 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, and for most of Citadel's history was completely benign and helpful.

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