In 2015, cloning technology has sophisticated enough to allow the copying of human organs and animals. Reproducing a complete human is explicitly forbidden by the "6th Day" laws, named for the day when god created man. Adam Gibson (Schwarzenegger) is a pilot who runs a charter helicopter business with his friend Hank Morgan. Michael Drucker, the owner of Replacement Technologies, a conglomerate that specialize in cloning, charters them for a skiing trip. Due to Drucker's financial and political influence, both Gibson and Morgan undergo blood and eye tests prior to his arrival to verify their identities and aptitude. On the day of Drucker's arrival, the same as Gibson's birthday, Gibson finds that his family dog Oliver (which belongs to his daughter Clara has died, and Morgan offers to take his place as Drucker's pilot to allow Gibson a chance to run out and get his pet cloned. Gibson disagrees with the idea of cloning the dog, but takes a look in Re-Pet anyway. After hearing the sales pitch about cloned pets, he decides to think further about getting Oliver cloned and gets instead gets a Sim-Pal for Clara.
Gibson later returns home and discovers Oliver had already been cloned, suspecting it was his wife Natalie who went ahead with the Re-Pet. He almost enters the house when he sees what could only be a clone of himself already celebrating with his family. While sneaking around outside his own home Gibson is confronted and chased by Replacement Technologies security agents Robert Marshall, Talia Elsworth, P. Wiley and Vincent Bansworth, who are all trying to kill him. He is able to escape and seeks refuge at Morgan's apartment. He speaks with Morgan for a few minutes when Morgan is suddenly shot by Tripp, an anti-cloning fundamentalist. Tripp reveals that the Morgan he shot was actually an illegal clone. Tripp tells Gibson he had killed both Morgan and Drucker on the mountaintop earlier that day. Tripp then commits suicide to avoid being captured by Drucker's security team, shooting himself in the head so they could not scan his memory in search of other anti-cloning activists.
Gibson sneaks into Drucker's company and finds Dr. Griffin Weir, the scientist behind Drucker's human cloning technology. He explains to Gibson that Drucker and Morgan were both killed earlier that day, and were cloned to cover up the incident using a memory scan captured during the medical and eye exams the pilots took. However, they believed that Gibson was flying the helicopter and they accidentally created a Gibson clone before they realized their mistake.
Drucker's security had been trying to kill Gibson to keep Drucker's illegal cloning operation a secret; if it was discovered that Drucker was just a clone, he would automatically lose his vast company, since clones cannot own anything. Weir also reveals that Drucker's human clones are embedded with a fatal disease that would kill the clone after five years, thus giving Drucker leverage to continually cloning them. Weir only discovered the disease protocol when he found out that his wife - who he had cloned after her death five years ago - was dying of a traditionally childhood disease. Weir confronts Drucker and tells him he wants to quit, stating that he has promised his wife that he would not clone her again. Drucker kills Weir, intending to later clone Drucker and his wife, but with their recent memories erased.
Drucker orders his agents to take Gibson's family to make sure he cooperates with the cover-up. Gibson devises a plan with his clone (who believes he is the original) to destroy Drucker's facility, rescuing his family in the process. Drucker forces Gibson to surrender and informs him that he was the clone all along. Drucker tries to convince Gibson's clone to reveal where the real Gibson was hiding, since he had all of Drucker's cloning memory hard drives. Drucker tries to stop Gibson, which causes the deaths of Marshall, Elsworth, Barnsworth and Wiley. Gibson and his clone trick Drucker into a trap, leading to Drucker's final death while the cloning facility is destroyed. Gibson escapes the complex with the inflammatory information. The original Gibson arranges for his clone to move to Patagonia, Argentina, to start a satellite office of their charter business, and to keep the clone's existence under a secret.