With control of XERXES' systems, SHODAN discovered that the Many had wrapped its biomass around the Von Braun and the Rickenbacker, locking the two ships together. Soldier used Malick's quantum chips to give SHODAN control of XERXES' Simulation Units, and used the Resistance's makeshift transmitter to pull power away from XERXES. Furthermore, SHODAN tasked soldier with sabotaging the XERXES system, so that she could assume control of the Von Braun's systems. She informed soldier that destroying the Von Braun was the only option, but not without transmitting her consciousness to the Rickenbacker first. SHODAN issued an ultimatum to the soldier, stating his only chance for survival lay in destroying the Many for her. While the AI went into forced hibernation, the Many evolved beyond her control. A sliver of SHODAN's memory was contained in the Grove, which survived on a Data Wafer which Bayliss later brought aboard the Von Braun.

Thirty years later, the Grove landed on Tau Ceti V, where it would be discovered by the Von Braun. The Hacker ejected Beta Grove to prevent SHODAN from using her experiments to conquer Earth. SHODAN explained that she was responsible for creating the Many, them being the results of her bio-engineering experiments on Citadel Station's Beta Grove. In reality, Polito had committed suicide days before, and the AI assumed her identity in a misguided attempt to establish trust between the soldier and herself. When soldier reached Ops, SHODAN dropped her facade and began taunting him. After a further detour through Hydroponics, which the Many have transformed into a hatchery for their Annelids, soldier used a chemical to push back the Many's growing biomass and unclog the elevator shaft. Advised by Polito, soldier restored the elevator to working condition, only to discover that the elevator shaft above the Hydroponics Deck was blocked by the Many's growing biomass. However, the Von Braun was crippled by the Many, the ship was on security lockdown, the main power was off and the elevator shaft was shut down by a series of malfunctions on the Engineering Deck. After his awakening, soldier's main imperative was to meet with Polito on the Operations Deck two floors above.

System shock hacker