Arnold Schwarzenegger as The Terminator: Reprising his role from the first two films. This film was Arnold Schwarzenegger's final starring role before becoming Governor of California.

Because of the events shown in the second film, Judgment Day did not occur as originally predicted. However, John Connor (Nick Stahl) still doesn't believe the future war has been totally averted. He is living "off-the-grid," in Los Angeles, California with no permanent residence, credit cards, or mobile phone, and is working freelance so he can't be tracked. Skynet sends another Terminator, the T-X (Kristanna Loken), back to July 24, 2004, Judgment Day, to kill the human resistance's future lieutenants, because Connor could not be located through any information databases. The T-X, later dubbed the "Terminatrix", is armed with a full arsenal of advanced weapons from the future, avoiding the restriction of non-living tissue by carrying them internally, including the ability to remotely control most machines.

As before, a reprogrammed Terminator (Arnold Schwarzenegger), identical to the Terminators from the previous films, has been sent back in time to protect Connor and his future wife, Katherine Brewster (Claire Danes). In a plot twist, this particular Terminator killed John Connor in 2032, before being reprogrammed and sent back in time by Connor's wife. After rescuing them from an initial attack, the Terminator leads them to Sarah Connor's coffin, which her friends filled with weapons in the event that Judgment Day was not prevented. The T-X and the police arrive, and the three narrowly escape in a hearse.

After the destruction of Cyberdyne Systems in T2, the Air Force has taken over the Skynet project as part of its Cyber Research Systems division, headed by General Robert Brewster, Kate's father. In an attempt to stop the spread of a computer supervirus, they activate Skynet, allowing it to invade all of their systems. John, Kate, and the Terminator arrive just a few minutes too late to stop them. The T-1 terminators, under control of the T-X, start killing office personnel. John, believing that Judgment Day can still be stopped, asks where the Skynet system core is, and just before General Brewster dies, he tells John and Kate to go to Crystal Peak, a base built into a mountain.

As they board a plane to leave, they are attacked by the Terminator, which was reprogrammed by the T-X to kill them. To avoid killing Connor, it shuts itself down. When they reach Crystal Peak, they are attacked once again by the T-X. Suddenly, a helicopter comes crashing through the front wall and into the T-X. The Terminator has managed to reboot himself and regain control. The T-X detaches its legs as they are stuck underneath the helicopter, quickly crawling after John and Kate. The Terminator manages to catch hold of it and save John and Kate by detonating its last remaining hydrogen fuel cell in the T-X's mouth, destroying them both.

John and Kate discover that the base does not house the Skynet core. It is a Cold War era fallout shelter for government VIPs (including a podium for the President). General Brewster sent them there to protect them. There is no Skynet core; Skynet is software running on thousands of computers throughout the world, making Judgment Day unavoidable. Skynet launches nuclear missiles, starting the war of human versus machine. Foreshadowing Connor's future leadership role, when the confused military forces from Montana Civil Defense and amateur radio operators ask for orders, he picks up the radio and takes command.