When a computer supervirus disrupts all global communications systems, Brewster is hesitant to bring SkyNet online to combat it as he prefers to keep human beings in control rather than trust a machine to run everything. However, when military systems are threatened by the virus, Brewster is forced to make a decision and allows SkyNet to gain full access the US military's systems.
After throwing the switch, Skynet becomes self-aware and brings all computers under its control while the general is approached by his daughter Kate and suddenly witnesses her getting shot. He turns around to find the shooter with his daughter standing beside him, but doesn't have long to question this as the T-X - which had disguised itself as Kate - gets up and shoots the general. The Terminator blasts the T-X with a grenade launcher and sends her plummeting down an elevator shaft. Kate and John Connor tend to Brewster, who tells them that SkyNet has been infected by the virus. John informs Brewster that SkyNet was the virus all along and now that it has control of the military's systems, it will soon launch a nuclear attack.
General Brewster urges John and Kate to take him to his office where there is a file that can help them. The group manage to evade the T-1 robots rampaging through the complex and find the general's office, locating the file on Crystal Peak. Brewster tells John to look after his daughter and apologises to Kate for "opening Pandora's Box". He then succumbs to his bullet wounds and dies in Kate's arms.