The Machine tracks anomalous activity from San Francisco to Owen Island, NY, which is in the middle of a coming storm.
In New York, Finch and Reese take Bear to the movies on a rainy day. They haven't heard anything from Sam, and it's been three days since The Machine has sent them a new Number. Finch wonders if it has something to do with the virus that Kara uploaded before her death, and admits that he can't access The Machine to check on it. A nearby street phone rings and The Machine rattles off six Numbers. They go back to the library and Finch confirms that there's no connection between the six men. Three of them are listed on the missing persons database and two have disappeared entirely. The sixth man, Jack Rollins, is an antiques dealer in Brooklyn and hasn't been reported missing. Reese leaves to check with him while Finch calls to have Carter check on the other five.
Reese arrives at Rollins' apartment and finds no sign of the man. Someone has torn up the place and discarded a bill for a rental property on Owen Island. Finch has checked Rollins' Visa account and confirmed that he left the city in a hurry. Reese heads for Owen Island despite the coming storm.
At the station, Carter calls in SAIC Agent Moss and has him provide the FBI files on the missing men. The first one was a French student who disappeared seven years ago. Special Agent Fahey is listed on all of the reports and Moss explains that Fahey handles cybercrimes and identity theft. Fahey left a lot of notes and Carter tells Moss that she'll handle the follow-up. As he goes, Carter asks Moss what is going on with Cal Beecher. Moss admits that he doesn't have access to the IAB files but he's seen enough red flags to figure that Cal is bad news.
Carter calls Fahey and asks him about the pattern he found about missing or destroyed photos at several potential crime scenes. Fahey says that no one reads his reports and he put all of the information together months ago, but no one in the NYPD was interested. Carter claims that she has a confidential informant that has brought it to her attention, but Fahey tells her to call the FBI liaison if she wants to pursue the matter.
Reese makes it to Owen Island and goes to the rental house. He checks in with Finch, who has gone to Rollins' house during a blackout. Finch tells Reese about what Carter found out as he looks for any photos. He finds keys to the basement storage area and goes downstairs with Bear. Finch finds empty photo frames and tries to tell Reese, but the signal cuts out. At the rental house, Reese hears someone moving.
At Rollins' house, Bear barks at the furnace and when Finch opens it, he finds several human teeth among the ashes. Meanwhile, Reese comes face-to-face with an armed man. The man flashes his FBI badge and identifies himself as Agent Fahey. Reese shows him his stolen U.S. Marshal badge and they realize they're both looking into another in a strong of missing persons cases. Fahey says that he just got there and they agree to lower their weapons and check the house. As they search Fahey explains that FBI wasn't interested in Rollins' disappearance so he came to check it out on his own. They confirm that Rollins was there recently and Fahey suggests they go to the local police station and get some help.
Finch goes back to the library and calls Carter in. She explains that the fire wasn't hot enough to destroy enamel, but warns that it will take a while to get an ID from them. Finch figures that they're looking at a string of murders and realizes that the killer would be a composite of all of the missing persons. Since he can't get through to Reese by phone, he prepares to fly to Owen Island to warn him that they're dealing with a killer.
Reese and Fahey meet with Deputy Erica Schmidt, who explains that she's in charge handling the evacuation while the chief of police is on the mainland. Erica tells them that if Rollins was a renter then he's already been evacuated. She tells them that the evacuation is her priority and goes back to work, and Fahey tells Reese that he figures Rollins is dead and they're after a serial killer. He then asks Reese what he knows about making a body disappear.
Cal comes to the station to see Carter since she's been ignoring his calls. She says that she's busy with a case and will talk to him later, and Cal leaves.
Two of the residents, Carly and Kyle Moon, come to the station when their engine died. Reese tries to ignore the overly chatty Kyle and asks Fahey what he meant earlier. Fahey explains that he started with the Stanford student and has determined that each victim of the killer moved after 18 months and disappeared. He went to Rollins' apartment, found the property bill, and came to Owen Island.
Locals Stan Amis and Becky Hess come in with Dennis Cunningham, and Stan explains that the bridge is out and they can't cross until the tide goes down. Erica realizes that Dennis is in town building a new hotel. Stan says that they saw someone at the dock prepping a boat for himself and Reese and Fahey leave to investigate.
When they get to the docks, Reese and Fahey find a man bringing in his catch. He says his name is Ethan Mattison but doesn't have any ID. Reese hears someone moving and calls out, threatening to shoot. A man, Victor Engquist, comes out and says that he was on the island looking for work and was stranded with the rest. As they go back to the station, Reese spots a small plane flying overhead.
Back at the station, Reese finds Erica putting Finch under arrest. He's claimed that he's an amateur storm chaser and landed in the center of town. Finch has a case of equipment and Reese asks Erica to book Finch after the storm. She agrees and asks Stan to put some more gas in the generator
As night falls, Reese and Finch talk privately. They compare notes and figure that The Machine sent the six Numbers so they'd realize that the killer takes on his victims' lives, gets bored, and moves on to the next victim. Finch figures that might be able to identify the killer by comparing him to his six victims. Stan comes back in and tells Reese that Fahey wants to meet with him out back. Fahey has found a pile of identity papers that the killer burned using diesel from the generator, and they realize the killer could be anyone inside.
Reese goes back and tells Finch what they've found, and Finch figures that the killer is trapped. He can't go anywhere with the ID he's stolen, and Finch figures that the killer electronically erased his persona. When Reese wonders what to do next, Finch takes him to his equipment.
In New York, Carter goes over footage from a camera outside of an apartment in Chicago. Cal comes in and asks if she's still busy, and Carter asks him to look at the footage. She explains that it came from a camera in Chicago six months ago and shows Rollins leaving his shop. Carter then runs footage of Rollins coming back the next day. Cal immediately spots that it's a different man based on his height and which hand that he uses, and Carter says that they're dealing with something much worse than robbery.
Reese asks Fahey to let Finch help them interrogate the others, while Finch rigs wiring to a chair. Fahey wonders why and Reese points out that Finch is the only one who arrived after the bridge went out. Finch explains that he has an instantel seismograph and Fahey seems to recognize what it is. He puts on body armor, telling Reese that he hasn't questioned dangerous killers before, and Reese assures him that he'll be standing right behind him.
Fahey and Reese call in the locals and question them about what has been going on and why they're on the island. As Fahey continues, Reese checks with Finch, who is using the seismograph fastened to the interview chair as a makeshift lie detector. Most of their readings are steady but Ethan is nervous about something. Meanwhile, Fahey interrogates Erica and she points out that no one has ever met Dennis, and that they don't get drifters in winter.
Carter sets up a web conference with Vicki Winters, the Dean of Student Affairs at Stanford. She remembers the missing French student, Henri Musset, and tells Carter that his disappearance drew international attention. There was a digital trail on Henry in San Diego 18 months later. Vicki confirms that in his last year Henri had a roommate, Alex Declan. Henri requested a new roommate in his senior year but the matter as then resolved. According to the files, Declan is listed as Henri's roommate but he was never registered at Stanford.
Fahey interviews Dennis, who explains that his hotel was behind schedule. Victor admits that he doesn't have any ID and was just passing through, and Reese points out that he has a lot of d-rings on his duffel bag. When Reese suggests that he was in the military, Victor becomes very nervous.
Carter calls Erica on the emergency frequency and asks to speak to Reese. Before Reese can get on the line, the generator goes out. He goes to check it out and discovers that someone has unplugged it. Reese plugs it back in and goes inside... and discovers that someone has stabbed Erica in the back, killing her. Finch notices that the killer has destroyed his equipment while he was out with the others.
As the group starts sniping at each other, Finch says that he needs time to work out the behavioral analysis data he gathered. Reese points out that the knife is a kabar, a military weapon, and everyone looks at Victor. He attacks Reese, who subdues him and reveals that he has a Marine tattoo. Victor admits that he was lying but he's no killer. Reese figures that he's on the run and Victor explains that after his second tour, he couldn't go back and tried to get a boat to Canada. When Victor says that he came in with Ethan, they realize that Ethan is gone and Reese tells Fahey to get the others to safety while he goes after the fisherman.
Cal drives Carter to the island and tries to talk about why she's avoiding him. She tells him that she got aced out of the FBI because she was keeping bad company. Cal assures her that he's in Narcotics and they get pulled in a half-dozen times a year. She says that she doesn't trust him and Cal speeds up, demanding to know what they told her about him. He finally slams on the breaks and sees that Carter has drawn her gun. She admits that she doesn't know if he would hurt her, but tells Cal that she doesn't want to hurt him.
Reese goes to Ethan's boat and checks the cage the fisherman was examining earlier. There is marijuana inside and Reese realizes what Ethan was trying to protect. Ethan steps out and fires a harpoon gun at Reese, missing, and Reese knocks him out before he can reload.
Finch goes over the readings and sees something unusual.
Reese drags Ethan over to Fahey's car and tells the fisherman that he doesn't have time to deal with him now. Inside the trunk he finds a dead FBI agent. Before Reese can react, Ethan recovers and knocks him out from behind.
Finch goes to the interrogation room and discovers that Fahey has discarded his ID. Fahey comes up behind him, puts a gun to his neck, and asks what gave him away. Finch explains that the needle spiked between interviews when "Fahey" was resting on the table. Declan realizes that Finch is more than a storm chaser and threatens to shoot the others if Finch puts up a fight.
Declan takes Finch out to the generator shack and Finch says that things are closing in. "Fahey" isn't concerned and explains that the real Fahey showed up at his door, looking for Rollins. The killer realized that Fahey knew too much and killed him. When Reese showed up, Declan had no choice but to improvise. He killed Erica because he didn't know what she heard on the radio Declan removes his contact lenses and asks Finch if he's an imposter like him. He removes Finch's glasses and puts them on, and Finch tells Declan that he's an amateur compared to him.
Ethan ties up Reese and drags him to the water's edge. Reese wakes up, grabs an oar, and knocks Ethan unconscious.
Finch warns Declan that he'll never get off the island and the FBI will come looking for the real Fahey. Declan says that they'll find the real Fahey, and tells Finch that he will fly him out. Finch says that Declan could never be him because he saves lives, and Declan insists that he kills people who waste their lives. When he finds the person he's meant to be, he'll stop. Finch says that people like him never stop and he hurts people because he likes to.
Irritated, Declan says that he'll find another way off the island and prepares to shoot Finch... and Carter arrives and shoots him down. Finch recovers his glasses and congratulates her on her timing, and Carter explains that she got a lift with the Coast Guard. As they talk, Finch remembers that Declan put on body armor earlier. The man gets up and prepares to shoot them... and Cal comes up and shoots him dead.
The next day, the storm clears and the police take away the bodies. Carter finds Cal looking for a bottle of whiskey. He pours himself and Carter a drink and asks what will happen between them today. Carter says that she doesn't know but admits that she's glad that Cal was there.
Finch meets with Reese, who tells him about Ethan's drug smuggling. Reese is satisfied that The Machine told them about the six victims, but Finch warns that the three days of silence indicates a glitch. If it had been working properly, The Machine would have given then the real Fahey's number and they might have saved him. As Finch wonders what that means, Reese says that the storm is passing and his friend warns that it's just starting.