In 1995, John Connor is living in Los Angeles with foster parents. His mother, Sarah Connor, had been preparing him throughout his childhood for his future role as the Human Resistance leader against Skynet – the artificial intelligence that will be given control of the United States' nuclear missiles and initiate a nuclear holocaust called "Judgment Day" on August 29, 1997 – but was arrested and imprisoned at a mental hospital after attempting to bomb a computer factory. In 2029, Skynet sends a new Terminator, designated as T-1000, back in time to kill John. The T-1000 is an advanced prototype made out of liquid metal (referred to as "mimetic polyalloy") that gives it the ability to take on the shape and appearance of almost anything it touches, and to transform its arms into blades and other shapes at will. The T-1000 arrives under a freeway, kills a policeman, and assumes his identity. Meanwhile, the future John Connor has sent back a reprogrammed T-800 (Model 101) Terminator to protect his young self.

The Terminator and the T-1000 converge on John in a shopping mall, and a chase ensues after which John and the Terminator escape together on a motorcycle. Fearing that the T-1000 will kill Sarah in order to get to him, John orders the Terminator to help free her, after discovering that the Terminator must follow his orders. They encounter Sarah as she is escaping from the hospital, although she is initially reluctant to trust the T-800. After the trio escape from the T-1000 in a police car, the Terminator informs John and Sarah about Skynet's history.[a] Sarah learns that the man most directly responsible for Skynet's creation is Miles Bennett Dyson, a Cyberdyne Systems engineer working on a revolutionary new neural net processor that will form the basis for Skynet.

Sarah gathers weapons from an old friend and plans to flee with John to Mexico, but after having a nightmare about Judgment Day, she instead sets out to kill Dyson in order to prevent Judgment Day from occurring. Finding him at his home, she wounds him but finds herself unable to kill him in front of his family. John and the Terminator arrive and inform Dyson of the future consequences of his work. They learn that much of his research has been reverse engineered from the damaged CPU and the right arm of the previous Terminator who attacked Sarah back in 1984. Convincing him that these items and his designs must be destroyed, they break into the Cyberdyne building, retrieve the CPU and the arm, and set explosives to destroy Dyson's lab. The police arrive and Dyson is fatally shot, but he rigs an improvised dead man's switch that detonates the explosives when he dies. The T-1000 relentlessly pursues the surviving trio, eventually cornering them in a steel mill. The T-1000 is frozen with liquid nitrogen and shattered, but manages to reform itself.

The T-1000 and the T-800 fight and the more advanced model seriously damages and shuts down the T-800. However, unbeknownst to the T-1000, the T-800 brings itself back online using emergency power. The T-1000 nearly kills John and Sarah but the T-800 takes it by surprise and blasts it into a vat of molten steel with an M79 grenade launcher, destroying it. John tosses the arm and CPU of the original Terminator into the vat as well. As Sarah expresses relief that the ordeal is over, the Terminator explains that to ensure that it is not used for reverse engineering it must also be destroyed. It asks Sarah to assist in lowering it into the vat of molten steel, since it is unable to "self-terminate". Although John begs and eventually orders the Terminator to reconsider, it makes the decision to disobey him, bids them farewell and hugs a tearful John before it is lowered into the vat, giving a final thumbs-up as it disappears into the molten steel. John and Sarah drive down a highway and Sarah says in a voice over, “The unknown future rolls toward us. I face it for the first time with a sense of hope. Because if a machine, a Terminator, can learn the value of human life, maybe we can, too."