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Clayton Verris plans to hunt down retiring assassin Henry Brogan. Because of that, he dispatches various assassins to kill him.
One day, Henry Brogan befriends agent Danny Zakarweski, a boat manager and hitwoman who remains loyal to him. When Clayton's hitmen invade Henry's home, he calls his spotter, Marino who then gets killed. Henry counts on Danny and both of them eliminate all of the hitmen.
They go abroad to the home of Henry’s former colleague Baron, and plan to meet with Yuri for further options. Clay dispatches his top assassin to kill Henry. Henry realizes the assassin bears an uncanny resemblance to a younger version of him, with a similar skill set. After a motorbike chase, Henry is outmatched and almost killed by the faster and more ferocious operative, until authorities arrive on the scene and the younger assassin flees. When the assassin arrives at a safehouse, he is revealed to be Clay's adopted "son" Junior. Curious about his similarities to Henry, Junior is ordered to finish the job.
Henry is also troubled by his similarities to Junior, whom Danny suggests might be his child, although Henry claims he isn’t married. From DNA samples of Junior, Danny discovers that his and Henry's DNA are identical – Junior is Henry’s younger clone. Desperate for answers, Henry meets Yuri, who informs him of the cloning project and that the man Henry killed was one of the project’s scientists who fled the US. Having designed a method to produce clones with no pain or emotion, the scientist tried to cowardly leave the US despite multiple baits and was killed upon being discovered. Junior, Danny and Henry later meet up in the museum, later followed by a confrontation.
To try and get Junior to turn away from Clay's intentions, Henry calls the head of his former agency, who agrees to send Junior to bring Danny safely back to the United States. Collecting Danny, Junior stalks Henry, but Danny warns him via covert listening device and Junior symphathetically gives Henry a shot of epinephrine.
Henry explains to Junior that he is a clone, convincing him by revealing their similar secret traits no one else could know. Escaping back to Gemini, Junior confronts Clay, who claims that he is better than Henry and is still Clay's son.
Finding Henry after defecting from GEMINI, Junior sides with him to defeat Clay with Henry urging Junior to quit in order to become someone better. A skirmish ensues and Baron is killed when one of the soldiers destroys the truck via flamethrower. Junior ambushes Clay, knocking him unconscious.
After defeating a wave of Gemini goons, Henry, Danny, and Junior face another younger clone, Senior, who feels no pain or emotion, managing to kill him. A defeated Clay tries to justify his actions towards Junior, who almost kills him, but Henry persuades Junior not to do so. However, Henry later kills Clay himself, having already lived with the heavy burden.
After Clay's death, the GEMINI Project was later decomissioned, meaning that no more clones will be produced and the remaining ones will be finally free from harm's way.
Clayton is a ruthless and murderous psychopath who has a kind and friendly facade, especially in front of his clone army. He served as a father figure and cared for Junior, who was reluctant to fight for him, right until the latter's betrayal.