As the launch of the grove tampered with SHODAN's experiments, she changed the jettison procedures to prevent more of the groves from being destroyed. However, SHODAN disabled the life support system in the launched Grove, resulting in their death.

Wishing to escape the chaos, a few executives fled to Gamma Grove and jettisoned themselves from the Station. Some of the mutants escaped, mutilated the medics and ransacked the armory. As inexplicable symptoms spread, Medical imposed quarantine measures. The patients started suffering from mental derangement and Security had to detain them to stop violent incidents. Eventually, SHODAN locked off Beta Grove and began her experiments. After that, systems and robots started suffering from serious malfunctions, flooding Maintenance with repair orders and causing speed loss in computer systems. Among several other serious malfunctions and haywire systems, SHODAN used a viral mutation agent experiment contaminating researchers and forcing crew shifts. 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 level 1