Lt. Parker Barnes (Washington) and another officer, Donavan, step off of a subway car. Their surroundings appear to be glitching as they run down a crowded city street. Donavan is not sure of where he is going, but Parker runs confidently into a Japanese structure. Donavan asks what they are looking for, and Barnes replies that they will know when they find a man with eyes like his own. They see a man (Crowe) sitting behind a screen, and they begin firing upon him. He jumps out of the way and grabs a gun of his own to return the fire. The foe snidely knocks out his partner and promises to return for Barnes. Barnes searches for him inside the building, but the man is able to surprise him and injures his arm. As Barnes recovers, the man taunts him, until Barnes is able to successfully shoot him in the arm. Unfortunately, the villain cheats and is able to gain the upper hand. The men disappear from the scene, and is is shown that they are in a virtual reality mechanism and in peril. The men are going into shock, and Donavan dies.
Wallace (Fichtner) and Elizabeth Deane (Fletcher) oversee the whole thing and argue about the failsafes before driving away. Parker claims again that the man, SID 6.7, cheated. He was not supposed to be able to electrocute people, as he found out by checking the database. The police chief, William Cochran (Forsythe) tells Barnes that he is trying to get him out of prison sooner, but all he wants is chalk. He then reprimands him for shooting another person within the program, but Barnes said that he wasn't real and he didn't want to end up like Donavan. Barnes then goes back to his automated prison cell, where it is revealed that he has a metal arm. He is forced to walk through a hall with many doors and people that are booing. A man emerges and attacks him with a knife, but Barnes wins handily and is dragged away by guards. Daryl Lidenmeyer (Spinelli), the program creator, approaches SID and tells him that he knows that he is the one that deactivated the protocols. SID says that killing was a real rush and refuses to be shut down. He says that in order to continue operations, Lidenmeyer needed to sacrifice his queen.
A therapist, Madison Carter (Lynch), comes in to give a psychological evaluation on Barnes. He claims that he was defending himself in the fight yesterday, and subtly mocks her. She reveals that she was watching his simulation yesterday to research a book that she was writing. He tells her that he knew that SID was in the restaurant due to the :) on the building. She states that they need to talk about Matthew Grimes, the man who killed his wife and daughter and took his arm. She claimed they needed to make sure that his act of violence wouldn't ever happen again, to which he replied that it couldn't because his family was already dead.
The scene cuts back to the testing lab where a woman in a robe is flirting with a man named Clyde (OConnor). She strips down to her underwear and begs him to come inside the program. Lidenmeyer approaches behind him and terminates the program, and offers to combine their technology of nanobots and AI to bring Sheila, the girl program, to life. Clyde agrees and goes to set up the necessary materials, while Lidenmeyer activates SID instead. SID begins flirting with Sheila, until Lidenmeyer deactivates him and takes out his module. He follows Clyde down to his lab where he shows him the nanotechnology that allows him to rebuild a part of a snake using glass. Clyde drops SIDs module, which he believes to be Sheilas, into a blue substance.
Parker lies on the floor of his cell with his chalk, and has flashbacks of his family.
SID is able to emerge from a shell into a nano body of his own. He immediately kills Clyde, and searches for Daryl who has fled out of fear. SID chops off his own finger and watches it regrow. The police chief vouches for Barnes to be able to catch SID out on the streets. They offer him a full pardon if he is able to catch SID in the real world, but he would be tracked for the rest of his life. He mocks them for thinking he would agree to be treated like an animal for their mistakes. However, allows them to place the microchip into his head. Carter says that she would like to go with Parker and threatens to go public if denied.
Barnes dislikes the idea of Carter going with him, and he states that he is not responsible for her if anything happens. She suggests that they start by investigating earlier models of SID to figure out his motives.
SID dresses himself in a suit in a room that contain the bodies of Mr. and Mrs. Henry Edwards. Barnes and Carter arrive at the scene to see the decapitates bodies and a message scrolled on the walls. They determine that SID is copycatting murders; starting with the Manson murders.
They go back to the building where they can run the earlier SID programs and learn that he is composed of almost 200 different murderers. Barnes is horrified to learn that one of these murders is Matthew Grimes. Carter comes back to her house to see her daughter, Karin (Cuoco), and Barnes cringes watching her. She calls Cochran to ask why Grimes would have attacked Barnes's family, when he was a political activist. Barnes was getting too close to his plans, so he kidnapped his family to throw him off. Karin approaches Barnes's car and they make small talk about baseball. (Simultaneously) SID goes to a club where people in leather are dancing and taking photographs. He approaches the main woman in leather, and then shoots the head off an automated bartender. He forces everyone down to the ground, shoots a man trying to run, and forces a woman to film him. Barnes picks up the news of SID's hostage situation and drives there with Carter. SID is recording peoples screams and cries to make a symphony. Parker leaves his vehicle to rush onto the scene. SID shoots four cops who come inside, and he alerts everyone that they are almost out of time. Parker arrives and empties his entire mag into SIDs back, who leaps onto an elevator, flicks him off, and escapes in a cop car. Parker jumps onto the hood of the car and shoots it as it races away. Carter follows and picks him up to chase him. SID eats the glass from the broken windshield to patch himself back back up. He giggles and crashes into cars along the road, while taunting Barnes through the police radio. He gets out and stands on top of the car and jumps over the side of the bridge.
Wallace complains to Deane about having to destroy the future of nanotechnology. Cochran scolds Barnes for shooting Sid that many times in a populated area. Deane, Barnes, Cochran, and Wallace discover that he is evolving into something new. SID walks through an electronics store and changes every TV to the news coverage of his attack from the previous night. A man switches the channel to watch his wrestling program, so SID breaks his neck while someone records on a camcorder. Carter and Barnes arrive at the store and discover that SID has probably gone to the wrestling match, due to the enormous number of people. The crew up in the control room have been slaughtered, unbeknownst to the crowd who is still cheering. SID flirts with a beautiful woman in the crowd and throws her boyfriend on the bottom floor. He backflips onto the floor and then into the ring, before spotting Parker in the audience and running out of the stadium. Parker chases him out of the building and onto a light rail. SID holds up a woman in front of him and taunts him while the rail pulls away. Barnes shoots anyway and the hostage falls down dead, and SID rides away on the train. The police put Parker in the back of a van to return him to prison. Parker tells Carter that SID is now mocking him with Grimess catchphrase; "This ones for you Parker", before killing someone. Carter checks the body and finds out that the woman was shot from the back, so Parker couldn't have killed him. She realizes that SID is trying to set him up and tells Cochran, but he doesn't believe her. Barnes is sitting in the van and has another flashback about his family. In it, Grimes is being interviewed by a reporter and spots Parker sneaking in through a window. Parker hears cries and rushes to find his wife and daughter locked up in a room with a bomb. They beg him to help them, but when he enters the room, a motion sensor sets the bomb off, killing them both and blowing off Barnes's arm. Barnes rushes in and kills Grimes's henchman and finally Grimes. The reporter and cameraman approached him from the back, and he turned around shooting blindly and killed them. Back in the van, SID arrives and talks to him through the grates.Then he opens the back of the van and throws Barnes the key. He reveals that the microchip in Barnes's head has the capability of killing him in 30 seconds, and then frames him for killing two guards before disappearing.
Barnes calls Carter to let her know hes with his family. Carter then calls Cochran who now believes that Barnes is innocent. She also tells him about the neurotoxin in the microchip. Wallace readies the satellite for the activation of the toxin, but Cochran busts in and destroys the machines.
Carter finds Barnes at his family's grave and they rush off to try to stop SID from his next demonstration at the largest television event ever. While people on the street are chanting about borders and guns, SID kills the men in the sound booth and tweaks controls to project Death TV. He then shoots a man in the head on camera. He states that he can do any kind of killing that the viewers want to see, but his first victim will be Karin Carter, Madison's daughter. Madison begins crying hysterically, so Barnes promises to find her, but she needs to find a way to cut off all phone lines to the building. SID states that Karin will be blown up in two hours, and the viewer number continues to rise. Barnes is spotted by the police, but escapes the gunfire by entering an elevator. Lidenmeyer returns from hiding, but Carter pistol whips him across the face.
SID puts a gun in a man named Ed's mouth, but releases him when the phone lines go dead. Barnes arrives and shoots SID many times, but he escapes through the ceiling. They exchange gunfire, and a helicopter threatens Barnes. Barnes shoots SID multiple times and they fight on the rooftops, before crashing into a glass building with glass sheets. The shards stuck through SID's body and separate his limbs. Barnes believes that he is incapacitated, and gets very close to him. However, SID grabs Parker and attempts to impale him, as well, while regenerating his arms and legs. Parker punches through SID's head and grabs the module; effectively disabling the antagonist. Carter walks in with Lidenmeyer, who states that Barnes has now ruined his chances of finding Karin. Parker stares into the module and relives the moment before the crash through the wall. However, this time, SID wins and throws Barnes over the wall and onto the pavement. Carter approaches SID who kidnaps her and takes her to her daughter. It is revealed that this time, Barnes and Madison are within the virtual reality mechanism, but SID does not realize this. SID flirts with Madison against a building that holds Karin. Daryl kills Cochran with a tire lever, which traps Barnes inside the simulation. SID sends Barnes into sensory overload in an attempt to kill him, so Madison shoots Daryl to help Barnes out of the mechanism. Barnes punches Wallace and unplugs SID, then tells Carter that they are going to save her daughter. Barnes avoids the booby traps by climbing in the fan in the top, but realizes that Karin is sitting on a press switch, so he cannot move her. Carter tells her daughter to remain very still. Barnes pulls a wire out of his arm and connects to to the computer box and successfully disarms the timer. The bomb squad neutralize the bomb and save the girl.