The Machine tracks a pattern of anomalies from San Francisco to New York and Owen Island off the coast. The island is currently under storm watch.
In New York, Reese and Finch go to the movies, bringing Bear in as a handicap assistant dog. They've had nothing to do for three days because The Machine hasn't sent them a new Number. Finch wonders if it's suffering from the virus that Kira uploaded into the U.S. computer systems. Reese suggests that he check The Machine but Finch reminds him that he programmed it so that it is inaccessible to maintain security. A nearby phone rings and Finch answers it. Once he takes down the information from The Machine, they go back to headquarters and discover that The Machine has sent them six Numbers. There is no apparent connection between the six and five of them are either reported missing or simply gone. The sixth man, Jack Rollins, is an antique dealer in Brooklyn. There's no indication that he's disappeared and Reese goes to check on him while Finch ahs Carter check on the other five men.
When Reese enters Rollins' apartment, he discovers that someone has torn the place up but there's no sign of the antique dealer. Reese does find a bill for rental property on Owen Island. Finch checks Rollins' credit card account and confirms that he left New York suddenly. Reese heads for Owen Island even though it's in the middle of the storm.
At the precinct house, Carter calls SAIC Agent Moss in with the files on the missing men. The first one was a French exchange student, Henry Musset, who disappeared seven years ago. Special Agent Fahey filed all five reports and Moss explains that Fahey handles identity theft cases. Carter tells Moss that she'll handle the follow-up and then asks the agent what he knows about Cal. When it's clear Carter won't back down, Moss tells her that he doesn't have anything specific but that he has seen Cal's numerous IAB files and warns her that her boyfriend is bad news.
Carter calls Fahey, who is in a parked car in New York City, and asks him about the files. She points out that there's a pattern of missing photos at each crime scene, but Fahey notes that the NYPD wasn't interested in the information he put together. When he wonders why Carter is interested, she tells him that she has a confidential informant who has turned up new information. Fahey refuses to discuss it with her if she won't give the informant's name, and tells Carter to call the FBI liaison for more information.
Reese arrives on Owen Island and checks on Rollins' rental house. Meanwhile, Finch has gone to Rollins' house and is in contact via phone. He tells Reese what Carter discovered and finds empty photo frames in the basement, matching the MO in the other five cases. They lose their signal and Bear starts sniffing at the furnace door. When Finch opens it, he finds human teeth and ashes inside.
At the rental house, Reese hears someone moving and goes to investigate. He finds himself face-to-face with an armed man, who identifies himself as Agent Fahey with the FBI. Reese shows him his stolen U.S. Marshal ID and explains that he's also looking into the missing persons cases. They agree to lower their weapons and Fahey explains that he just got there. His superiors weren't interested in Rollins' disappearance or its relationship to the other cases, so he came to Owen Island to check it out. The two men look around and confirm that Rollins was there recently, and Fahey suggests that they go to the local police station and requisition manpower to conduct a search.
Back at headquarters, Finch calls Carter after she's gone to Rollins' apartment. She tells Finch that the furnace wasn't hot enough to destroy dental enamel and warns Finch that it will take a why to get an ID. Finch figures that the man who killed Rollins also killed the other five missing men and that the killer may be incorporating their personalities into his own. He's still unable to contact Reese because of the storm and tells Carter that he's going to fly to Owen Island to warn his partner about what they're dealing with.
Reese and Fahey meet with Deputy Erica Schmidt, who explains that the chief is on the mainland supervising that end of the island evacuation. She doesn't have the time or interest to help them and figures that if Rollins was on the island, he was evacuated with the other renters. As Erica goes back to work, Fahey tells Reese that they're after a serial killer and Rollins is his latest victim, and then asks Reese what he knows about making bodies disappear.
Cal visits Carter at the station and complains that she's been ignoring his calls. She tells him that she's been busy and says that she'll call him later. Rebuffed, Cal leaves.
Carly and Kyle Moon, two newlyweds, come to the station when their engine dies. Reese tries to ignore them and asks Fahey for more information. The agent explains that he started with Henri and learned that 18 months later, someone using Henri's identity had moved eastward. Eighteen months later, "Henri" killed another victim, took his identity, and repeated the pattern. Fahey traced the killer to Rollins', found the rental bill, and came to Owen Island to find his target.
Locals Stan Amis and Becky Hess come in along with a businessman, Dennis Cunningham. Stan tells Erica that the bridge is covered over and they can't cross over until the tide goes down. Erica points out that Dennis is a businessman opening up a new hotel on the island. Before he can respond, Stan tells them that he saw someone at the docks prepping a boat to leave. Reese and Fahey go to investigate. When they get there, they find a fisherman, Ethan Mattison, checking his nets. As they demand Ethan's ID, Reese hears someone moving behind some crates and orders them out at gunpoint. The man, Victor Engquist, comes out and claims that he was on the island looking for work. Reese and Fahey take both men to the station and notice a small plane flying overheard.
When they get back to the station, they discover that Erica has arrested Finch for landing his plane in the center of town. He claims that he's an amateur storm chaser and had to put down. He has two cases of equipment with him and Reese suggests that they book Finch after the storm. Eric agrees and asks Stan to go in back to refuel the generator.
Once they have a chance to talk privately, Reese and Finch compare notes. They figure that The Machine sent them the Numbers of the six dead men that the killer "borrowed" his identities from. Once the killer gets bored with his new life, he moves on, kills another man, and takes their life. Finch figures that he might be able to pinpoint who the killer is by comparing him to his six victims and see what identity traits carried over. Stan comes back in and tells Reese that Fahey wants to see him. When Reese goes to the generator shack, Fahey shows him a pile of burned identity papers belonging to Rollins. They realize that the killer destroyed the evidence of his new Rollins ID and could be any of the people inside. Reese tells Finch what Fahey discovered and Finch figures that the killer is trapped. He points out his cases of equipment and tells Reese that he has a way to find the killer.
In New York, Cal comes back to see Carter, who is going over video footage of Rollins first entering and then later leaving his shop. Cal immediately picks up on the same thing that Carter did: the second man is taller and left-handed. When he asks if the man was a robber, Carter says that he's something much worse.
Reese asks Fahey to let Finch help interrogate the people trapped on the island, pointing out that Finch is the only one they know arrived on the island after the storm. The FBI agent agrees and Finch wires up an instantel seismograph that he brought with him. Fahey puts on body armor, telling Reese that he's never interrogated dangerous killers before, and Reese sarcastically tells him that he'll be there with him.
Fahey questions the stranded locals one at a time, asking them their business on the island. Reese checks with Finch, who is measuring each person's stress using the seismograph. He points out that Ethan is nervous about something but the others don't seem to be unduly nervous. Meanwhile, Fahey interrogates Erica. The deputy points out that no one has ever met Dennis before, since he's never come to the island to inspect his property until the storm. She also points out that if Victor were ordinary drifter, he wouldn't come to the island in the dead of winter looking for work.
Carter sets up a web meeting with Vicki Winters, the Dean of Student Affairs at Stanford University. Vicki informs Carter that Henri's disappearance drew international attention at the time. Carter has checked the records and confirmed that someone using Henri's ID turned up in San Diego 18 months later. Vicki confirms that Henri had a roommate, Alex Declan, in his last year. Henri requested a new roommate a short time later but then cancelled the request. According to the registrar files, Declan never signed up for any s at Stanford.
Fahey interviews Dennis, who explains that he only came to the island because the weather was putting his hotel project behind schedule. Next is Victor, who claims that he was just passing through and claims that he doesn't have any ID. Reese tosses the drifter's duffel bag on the table and points out that it has military-grade d-rings on it.
Carter tries to call the sheriff's office on an emergency frequency. Erica takes the call and the detective asks to speak to Reese. Before Reese can get on the line, the lights go out and he goes to check it. While everyone else gets together, Reese discovers that someone unplugged it and restores the power. When he goes back inside, he discovers that someone has killed Erica, stabbing her in the back. Finch checks on the radio equipment and discovers that the killer smashed it to piece.
Everyone starts arguing and Finch tells Reese that he needs time to review the stress data he measured. As he leaves the room, Reese checks the murder weapon and tells the other that it's a Army issue kabar. Victor attacks Reese, who easily subdues him and yanks down his sleeve, revealing a Marine tattoo. Victor admits that he lied about what he was doing but insists that he didn't kill Erica. He explains that he went AWOL after his second tour and was trying to get a boat to Canada. Victor notices that Ethan is gone and Reese tells Fahey to get the others off the island while he goes after the fisherman.
As Cal drives Carter to the island, he tries to get her to open up about her cold shoulder toward him. She finally tells Cal that Moss warned her about his IAB record, and Cal points out that since he's in Narcotics, he gets a half-dozen false accusations a year. As they argue, Cal speeds up, demanding to know what Moss specifically told her about him. He finally slams on the brakes when he notices he's lost control, and realizes that Carter is ready to draw her gun. When he wonders if she thinks he could hurt her, Carter says that she doesn't know but that she's sure she doesn't want to hurt him.
At the docks, Reese checks the nets that Ethan was at earlier and discovers that they contain marijuana. Ethan fires a harpoon gun at Reese but misses, and Reese walks over and knocks him out.
Finch goes over his readings from the interrogations and realizes that something is wrong.
Reese prepares to throw Ethan in the trunk of Fahey's car and deal with him later, but discovers that there's a corpse inside. As he stares in surprise, Ethan manages to knock him out from behind.
Finch goes to the interrogation room and discovers Fahey's ID on the floor. "Fahey" puts a gun to Finch's neck and asks what gave him away, and Finch explains that his equipment spiked when Fahey was leaning on the table. The killer, Declan, realizes that Finch isn't what he appears and orders him out to the shack. He threatens to shoot the others if Finch puts up a fight. Once they enter the shack, Finch warns Declan that time is running out for him. Declan tells him that Fahey showed up looking for Rollins, unaware that Declan had taken his place. He killed Fahey and burned the body, then traveled to the island to take over Rollins' rental property. When Reese showed up, he had to improvise. When Erica overheard the radio conversation, Declan killed her in case she heard something that would give him away. The killer takes out his contact lenses and asks Finch if he's also an imposter, and then takes his glasses and puts them on. Finch dismissively tells Declan that, compared to him, he's an amateur.
As Ethan drags Reese to the edge of the dock to throw him in, Reese recovers, grabs an oar, and knocks the drug smuggler out.
When Finch warns Declan that the FBI will come looking for the real Fahey, Declan tells him that they'll find the real Fahey's corpse. As for getting off the island, he plans to have Finch fly him in the plane. When the killer says that he plans to become Finch next, Finch tells him that he could never be him because he saves people. Declan insists that he only kills people that waste their lives, and that he'll stop when he finds the person he meant to be. Finch doesn't believe him, explaining that people like Declan never stop and that he hurts people because he likes to. Angry, Declan says that he'll find another way off of Owen Island and prepares to shoot Finch. Carter comes up behind him and shoots him in the back. Finch picks up his glasses and thanks her, and Carter explains that the Coast Guard gave her a lift. As they talk, Finch remembers that Declan put on body armor earlier... and the killer gets up and comes after them. Cal arrives and kills the man for good.
The next day, the storm moves out to sea and the police and FBI clean up. Carter finds Cal in the sheriff's office looking for a bottle of whiskey. As they share a drink, Cal asks what will happen between them. Carter admits that she doesn't know but she tells Cal that she's glad he was there.
Finch and Reese go back to Fahey's rental. They compare notes and Reese points out that The Machine did warn them. However, Finch is worried that The Machine didn't simply give them Fahey's Number, and realizes that the virus is impeding its function. Reese looks at the departing storm and says that it's passing, but Finch warns that the real storm is just starting.