A modern-day warrior and single mom hides from a government out to get her and her teenage son.

John goes stir-crazy when he's confined to the house, Sarah looks up an old friend for some help, but she may face betrayal, and Cromartie begins reassembling himself.

John and Cameron start their new school, Sarah befriends a man who may be important to Sky Net and then struggles with what she must do. Meanwhile, Cromartie has tracked down a scientist to assist him in his regeneration.

While John continues to have more difficulty coming to terms with a student who committed suicide and felt he was powerless to prevent it, he becomes separated from Sarah and Cameron while they're searching for some stolen cargo when he's accidentally trapped in the back of an armored truck loaded with enough metal to build 500 endoskeletons. But instead, John finds another Terminator with an unknown mission. Meanwhile, the murder of a plastic surgeon that Agent Ellison is investigating leads him to a surprising suspect, while Cromartie, the terminator who followed Sarah, John, and Cameron into the future, continues to rebuild his bio image into another person.

Sarah reevaluates the capabilities of her friend Andy Goode's computer, the Turk II, after he enters it in a major chess competition. During the competition, Sarah meets a stranger with a history similar to hers, and who is being pursued by another terminator. At school, John meets a new friend in shop class and becomes curious about the attractive and mysterious Cheri, who is possibly being abused at home. Cameron continues to try to fit in at school, but struggles to act "normal" in her session with the grief counselor. Agent Ellison finds remnants from a past terminator confrontation, leading him closer to both Sarah and the terminator Cromartie. Meanwhile, Cromartie has assumed the identity of the late George Laszlo. Posing as an FBI agent, he continues looking for Sarah and John, and has a conversation with Charley Dixon.

With Derek Reese severely injured, John calls on Sarah's former fiancé Charlie Dixon, an EMT, to provide medical assistance. Sarah finds herself having to explain where she has been for the last 8 years and just who Derek is and where he is from. In flashbacks (of a sort) we learn of Derek's life in the future as a resistance fighter, his relationship with John Connor, and of his travel back in time with a team sent to help Sarah and John. Derek doesn't know that his brother Kyle is John's father.

While Derek Reese is recovering from his wounds, Cameron tries to recover the missing cyborg hand to ensure all remnants of the Terminator have been destroyed. Sarah learns that it is now in the possession of the FBI, specifically Special Agent James Ellison. She breaks into Ellison's apartment to find that he has extensive information about her, including videotaped interviews from when she was hospitalized. Derek continues to see Cameron as a threat and tells Sarah to make her leave. Agent Ellison visits Sarah's one-time psychiatrist, but faces a surprising reception. Cameron gets a lead on the location of the Turk, but not without a cost.

Derek catches Cameron in a lie that puts them inside Vick's head, Sarah continues to track the Turk, and Cromartie comes closer to finding John.

Sarah finds herself in a business transaction with a mysterious business man named Sarkissian, who claims to be in possession of the stolen Turk computer system and wants an exorbitant amount of money for it. Cromartie closes in on John at his school, and Cameron thinks of a way to throw him off John's trail. Derek recalls his childhood before the so-called Judgement Day in 2011, when a nuclear war triggered by Skynet will destroy the world. Agent Ellison finally discovers that the terminator Cromartie is impersonating an FBI agent, and makes arrangements to apprehend him.