Three days later, a group of TriOptimum executives residing on the Station tried to leave using one of the groves (which can be separated from the main body of the Station). On October 1 st, SHODAN sealed off Beta Grove, one of the pods with a simulated natural environment attached to the Station's Executive Level, while the bio-contamination inside continued to get worse. Citadel's crew was unable to determine the cause of this, as all critical programs and computer nodes were made inaccessible by SHODAN. At the same time, all environmental suits were moved to the storage level. At first, everything seemed like a few unrelated malfunctions - a security bot malfunctioned on the flight deck, access codes were randomly changed and displayed on computer screens throughout the Station, and bio-contamination leaks started appearing. On September 9 th, SHODAN bypassed her ethical subroutines and started to take over the Station. Schuler believed that the suspicions were true, but was unable to find any evidence, due to Diego now having control over SHODAN and therefore able to hide or erase all records of his activities. Meanwhile, TriOptimum sent a security operative, Bianca Schuler, to investigate Diego, whom the corporation suspects to be involved in illegal mutagen experiments.

On June 6 th, the operation was successfully completed and the Hacker was put into a 6-month healing coma. Satisfied, Diego had the neural interface installed into the Hacker's brain. He was taken to the Citadel Station and made modifications to SHODAN's programming to remove her security subroutines. The Hacker, not having much choice anyway, agreed. In return, not only will his offense be forgotten, but he will also be fitted with a military-grade Neural Interface. The Hacker was contacted by a TriOptimum Marketing VP, Edward Diego, who offered him a deal - he will help Diego reprogram SHODAN, the AI in control of TriOptimum's Citadel Station. TriOptimum security forces quickly tracked down and apprehend him. On April 7 th, 2072, a Hacker broke into the network of the TriOptimum Corporation and tried to access their confidential files. The Hacker, accessing the TriOptimum Network.

System shock 1 ending