Sarah Connor struggles to keep her 15 year-old son John safe from an enemy Terminator from the future in order to stop the rise of the machines. She uproots their lives and takes him to live in a small town in New Mexico where he befriends Cameron, an enigmatic and otherworldly high school student who ultimately becomes his protector. Meanwhile, FBI agent James Ellison is hot on their trail but may become a powerful ally.
Sarah makes contact with an old friend to ask a favor, while John decides to pay a visit to Sarah's ex and Cameron makes a new friend. Together they infiltrate a resistance safe house and discover they are not alone. Meanwhile, Agent Ellison realizes that Sarah is still alive and a dangerous person from Sarah's past is reawakened.
Sarah pays a visit to Miles Dyson's widow looking for Skynet's creators. Her search leads her to Andy Goode, a cell phone salesman who also happens to also be the inventor of a chess playing computer known as "The Turk.
When Sarah, Cameron and John track down stolen cargo, they become separated and John discovers the future isn't as safe as he had hoped. Meanwhile, Agent Ellison's murder investigation leads him to an interesting suspect.
When Sarah's friend Andy submits his computer into a chess competition, she revaluates his computer's capabilities and worries where it could all lead. During the chess match, Sarah comes face-to-face with a stranger whose history is closely tied to hers. Meanwhile at school, Cameron gets called into grief counseling and John makes a new friend in shop class. Agent Ellison discovers remnants from a terminator battle.
While fighting for his life and moving in and out of consciousness, a stranger remembers life in the future and his personal battle against the machines. Meanwhile, Sarah finds herself trying to explain the past to Charley.
When Sarah breaks into Agent Ellison's apartment looking for a missing endo-arm, she discovers dossiers, files and video from her stay in the mental hospital. The files lead her to hospital psychiatrist Dr. Silverman, a doomsday convert who made Sarah's hospital stay unbearable. Meanwhile, Cameron enrolls in a ballet class taught by Maria Shipkov, Dmitri's sister, in an effort to track down his whereabouts and to find out who has the Turk.
John defends Cameron against a damning accusation by Derek, putting him and Derek at odds, while Sarah finds herself in a business transaction with a mysterious business man.
In the season finale, Cromartie closes in on John and Agent Ellison discovers a nemesis at the agency.