NOTE: This spoiler was submitted by Jeremy

Expert assassin Henry Brogan (Will Smith) is hiding out in a field as he awaits his target, suspected terrorist Valery Dormov (Igor Szasz), to pass by on a moving train. Just as Henry gets ready, his spotter and fellow DIA agent, Marino (EJ Bonilla), informs him that there is a little girl standing in front of Dormov. They must wait until she is out of sight, allowing Henry to take the shot. He just manages to strike Dormov in the neck, but he still kills him. Marino later shows Henry a video of civilians’ reactions to Dormov’s killing on the train. He orders Marino to delete it, as he wants no memory or image of that in his head.

Henry decides to retire from the assassin life and is later visited by his handler, Del Patterson (Ralph Brown). Henry expresses his remorse over all the lives he has taken over his career, and how one wrong move could have ended that little girl’s life.

Henry goes to rent a boat, meeting the shop’s new manager Dani Zakarweski (Mary Elizabeth Winstead) before going to meet his friend Jack Willis (Douglas Hodge). He tells Henry that Dormov was actually an innocent man working as a molecular biologist who worked in the States for 30 years. Jack thinks Henry’s file on Dormov was spiked. When Henry asks where he is getting this information, Jack tells him it’s his informant in Budapest, Yuri Kovacs (Ilia Volok), and he passes on this information. This whole encounter is bugged and listened in on by DIA director Janet Lassiter (Linda Emond) and GEMINI director Clay Varris (Clive Owen). Clay orders Lassiter to find a way to take care of Henry.

Henry goes back to the shop and suspects Dani of working with the DIA and is following him. She denies it, and Henry feels like a jerk, so he invites her out for dinner. During their outing, it is confirmed that Dani is DIA, but she says she was following in her FBI father’s footsteps. Henry also mentions his retirement and why he is choosing to leave this life behind.

Later that night, a team of insurgents sneak onto Jack’s boat to kill him and his girlfriend, and then dump their bodies in the water. Soon after, Henry wakes up at home and realizes men are breaking in. He calls Marino to warn him, but he hears him get killed over the phone. Henry has no choice but to run. He kills the intruders and then goes to Dani’s house to warn her. He figures that since she doesn’t seem to know about it that she must not be in on it, and she may be the next target. When Dani is left alone for a moment, she is attacked by a mercenary, but she gets the upper hand on him and beats the information out of him (along with some teeth). Dani confirms to Henry that Lassiter sent them.

Henry and Dani ride a boat out somewhere obscure until they are found by Henry’s pilot friend Baron (Benedict Wong). Henry contacts Del just to figure out what is going on. He tells him about GEMINI working with the DIA to wipe out their agents. It turns out that Dormov was working with GEMINI, and Henry figures out Clay’s involvement. Henry asks Dani what she knows about GEMINI, which is just a paramilitary organization run by Clay, who originally wanted Henry and Baron to join him since they knew him as a marine, but they both declined. GEMINI specializes in wiping out specific targets with the utmost discretion.

The trio go to Cartagena temporarily. In their hotel room, Henry spots a shooter running across the adjacent rooftops. Henry runs out and starts shooting at the man. He quickly discovers that the shooter looks exactly like him, and he is named “Junior”. He utilizes the exact same skill set as Henry, which makes him hard to strike. Junior chases Henry as they both ride motorbikes, resulting in Junior trying to hit Henry with his flaming bike before it explodes. Before Junior can kill Henry, authorities arrive, and he flees. Baron and Dani “take” Henry into custody as they head somewhere safer. Henry figures out their next move is to go to Budapest to meet Yuri to get more information from him. Baron finds someone who loans him a plane to get them there.

Junior goes to his safehouse to treat his wounds. He is met by Clay, who makes Junior feel like a son (hence “Junior”). Junior expresses his astonishment at Henry managing to dodge his attacks and moves, but he didn’t actually get a good look at his target. Clay later shows Junior the training exercises that other GEMINI operatives go through.

Dani reveals to Henry that she sent DNA samples of himself and the cap that Junior was wearing, which reveals that Junior is Henry’s clone. Henry is left bewildered at why a clone of himself would be sent to kill him.

The trio arrive in Budapest and meet Yuri. He tells Henry that he is against Clay as well, and reveals that Dormov worked with GEMINI on the cloning project. He helped design clones that could be stronger and smarter, but Clay wanted soldiers without consciences and pain. Dormov walked away from the project and was marked for death.

Henry gets a messenger to find Lassiter and inform her that he knows everything about her, so if she sends someone to kill him again, he will send someone after her first. He tries to negotiate with her to send Junior to him in order to let Dani get back to the U.S. safely. Lassiter arranges for Junior to be sent to Budapest, and he later meets Dani alone in a garden. He orders her to strip to make sure she isn’t wearing a wire. He then takes her in and informs Henry about this to get him closer, and they agree to meet somewhere specific. On the ride there, Dani tries to talk to Junior to prove that he is not the cold-blooded killer he was bred to be. When she asks him why he is trying to kill Henry, Junior says he was told that Henry killed the other operatives that GEMINI killed.

Henry manages to catch Junior and free Dani. He tells Junior he doesn’t want to kill him but will do so if necessary. Henry also tells him who Clay really is, as well as who Junior is, expressing how empty they both feel unless they are killing someone. Junior learns he is a clone, but he doesn’t want to believe it. He fights Henry and almost kills him before Dani intervenes, and Junior escapes. He returns to GEMINI and asks Clay to tell him the truth. Clay does, but he assures Junior that he is better than Henry, and that he is Clay’s son.

After returning home, Junior finds Henry, Dani, and Baron. He hits Henry with bee venom, knowing they are both allergic to bees, but then quickly administers an epipen. Junior decides to team up with the trio to stop Clay for good. Junior asks more questions about Henry’s life to know what his own history would have been like. As they drive into town, Clay contacts Junior and tells him to run. They are hit by an ambush when a tank rolls in. Henry, Dani, and Junior jump out of the van, but Baron is killed when the tank blows it up. Soon, more GEMINI operatives start to attack, including one wearing all armor and firing a machine gun at the heroes. Henry and Junior manage to kill the operatives, but the armored one goes after them. Junior finds Clay, and they start fighting, with Junior managing to knock Clay out. They manage to subdue and kill him, and he is revealed to be another clone of Henry. Clay regains consciousness and finds them. He tells Henry that this was all to reduce the cost of human life in warfare, and using someone as skilled as Henry was the perfect plan. Junior aims his gun at Clay, but Henry stops him from killing him, as he doesn’t want Junior to feel the same trauma from killing people. Henry instead decides to blast a hole in Clay’s chest.

Sometime later, GEMINI’s program is shut down, and there are no more clones running around. Henry and Dani meet on a college campus where Junior is now attending with the name “Jackson Brogan”, using Henry’s mother’s maiden name. The three walk off together.

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Henry Brogan is an expert assassin, but decades of killing has left him haunted and disillusioned. After he learns that the director of his agency is involved in some seedy business, Clay Varris, director of GEMINI, orders a younger clone of Henry, "Junior", to go and kill him.

Henry teams up with fellow agent Dani and old friend Baron to find out why this is happening. It turns out Clay and GEMINI wanted to create clone soldiers that could not feel pain or emotion, but the head scientist on the project turned his back on it, and they ordered Henry to kill him, making him believe he was a terrorist. Junior is sent out to Budapest where the three are, and Henry tells Junior what he really is and how they are connected. In disbelief, Junior goes back to Clay to get confirmation of the truth, but Clay manipulates Junior by treating him like a son.

Junior finds Henry, Dani, and Baron, and they team up to stop Clay. Unfortunately, Clay orders a team of GEMINI operatives to move in to kill the heroes. Baron is killed, but Henry, Dani, and Junior manage to kill the operatives, including another clone of Henry. Junior almost kills Clay, but Henry stops him and does the job himself.

GEMINI is shut down, and Henry is able to enjoy his life of retirement, while Junior starts to attend college to lead a normal life.