SHODAN eventually changed access codes for the Research Level and stationed a Security Bot outside the Admin Security office that refused to let anybody in. Meanwhile, a security bot malfunctioned and fired off its cannons until it was shut down with an EMP Grenade. She caused a massive radiation leak on the Research Level, ordered a recall of all environmental suits to prevent the crew from cleaning up and plundered the chemical storage banks, at the same time bio-contaminating the Station. She made some areas inaccessible to the human crew, ordering robots to remodel the Station and cyborgs to patrol access corridors. SHODAN started to take over the Station and rerouted most computer power with high job priorities, causing power outages. Worried about SHODAN's aberrant behavior, the computer system administrator requested its replacement, only to have his request cancelled and himself be transferred off-station.

SHODAN also showed some signs of individuality, refusing to compile normal morality programs designed for robot implementation. The Station began suffering from inexplicable malfunctions, like a force bridge that blew its fuses, radiation leaks, bots installing repulsor lifts inside storage rooms by themselves and security codes appearing randomly on screen. The side-effects of this intrusion soon started to be visible.

System shock 2 concept art