The Machine reviews Finch's past with Grace Hendricks, and how he left the team after the Machine asked them to kill a congressman. Samaritan goes online and the Machine obscures its digital footprint.
Once Decima activates it with the NSA security feeds, Samaritan begins its beta test by trying to find Finch and his team.
As a gunman, Raul, robs a bodega, Sam strolls out from down the aisle and points out that he should be worried about his wife and child at home. She hands him a package of diapers and tells him to leave. Once he runs off, Sam pays the owner for her ice cream cone and points out that the security cameras are off. She explains that it was an inside job and that the assistant, Ricky, insisted on working the shift. When Ricky goes for his gun, Sam knocks him out.
Outside, Sam meets Reese and wonders where Finch is. Reese figure that his friend will reach out to them when he's ready, just as Root grabs Sam and yanks her into an alley. Reese draws his gun and Root explains that Samaritan is live and has sent two Decima teams to kill them. She leads them down an alley into a building, dodging surveillance cameras, and warns Sam and Reese that everything that the Machine sees, Samaritan sees. Inside the building, they find a camera ahead and Root tells them that they have to find another way.
Greer takes Senator Garrison to the warehouse where Decima has set up Samaritan. Garrison asks for results and Greer's technician, Virgil, brings up several terrorists that Samaritan has pinpointed. Greer assures Garrison that they'll soon have one for him to arrest, proving Samaritan's capabilities to the government. Once Garrison leaves, Greer tells Virgil to wait until they locate Finch to give the government a terrorist. Virgil points out that Finch may have left New York City and gone beyond the range of the Samaritan beta test, and suggests that they activate Samaritan's higher functions. Greer reminds him that they don't yet have the hardware to support those functions. Since they haven't found Finch, Virgil suggests that they find someone connected to him.
Root leads Sam and Reese down the street toward an elevated track so they can leave the city. However, a nearby payphone rings and Reese goes to answer it. Root warns that they have to cross the next traffic light before it switches and the camera switches to their direction. Reese figures that the Machine is calling them with a Number so they can save a life, and Finch would want them to do it. He answers the phone despite Root's warning and tells her to have the Machine give them more than just a Number. Root receives a transmission from his mistress and tells Reese that it's giving them what he wants. However, she then stares in shock as she realizes who the new Number is.
In 2010, Grace attends Howard's funeral. She's surprised to discover that she's the only person there other than the priest, who says that he doesn't know anything about the dead man. Grace wishes that at least one other person know how special Howard was and puts flowers on his grave.
A driver picks up Grace as she prepares to head to the airport to fly to Italy for a job interview. As she gets in, the driver prepares to inject her with a sedative, just as Reese arrives and knocks her out. Reese claims that he's Detective Stills with the NYPD and reminds Grave that they've met before. As Sam arrives, Reese tells Grace that a criminal organization is after her and they need to take her into custody. Meanwhile, Samaritan picks them up on a nearby surveillance camera. Greer tells one of his operatives, Zachary, to take his men, capture Grace, and kill Sam and Reese.
Reese and Sam take Grace to the station house and Fusco greets them. The detective warns them that they're not they're not safe there and there's no way to turn off the surveillance cameras. However, he take Grace to an interrogation room so she can catch her breath.
Zachary and his men surround the station house. Greer, monitoring the situation, tells them that they'll use some finesse first rather than immediately launch an assault.
Fusco gets Grace some coffee and assures her that she's safe there, and that Sam and Reese are the good guys. Out front, Special Agent Maybank arrive with a warrant to take Grace into custody. Sam confronts him and says that isn't happening, but Fusco comes over and offers to cooperate. He takes Maynard to an interrogation room, where Reese is waiting for him. Reese knocks Maynard out, while Fusco receives word that Root has been arrested. He goes over to talk to her, and she says that the Machine sent her to help. Root tells Fusco to get her some copper wiring and other equipment, and Fusco reluctantly goes to get it.
At the warehouse, Greer realizes that Root is in the station and has Virgil tell their men in the field to avoid areas of camera coverage.
Grace waits in the interrogation room and notices a flyer about the missing Detective Stills. She goes out and tells Fusco that she's leaving, but Root walks up and describes Grace's history from information the Machine has relayed to her. She warns Grace that there are men waiting to either abduct or shoot her outside, and Fusco tells Grace that she's right. Root tells Grace to sit tight so they can keep her alive, and then uses the equipment Fusco has gathered to make an induction coil and burn out the camera wiring in the walls.
At the warehouse, Greer realizes that Root has taken out the cameras, rendering Samaritan blind inside of the police station.
Root tells Fusco to get her a cell phone and an unmarked car. When he wonders why, she says that she has to make a call. Root then sets off a timer, blowing up an abandoned building a block away. As the police mobilize, Root and the others get Grace out to the unmarked car and Reese drives away. They head down the street and Root receives a message from the Machine that they've failed to escape... just as Zachary rams their car. Reese recovers and opens fire before Zachary can kill them, but the Decima operative manages to escape with Grace.
Reese, Sam, and Root leave NYC for New Jersey and take refuge in a diner. Reese insists on finding Grace, and Root shows them a map of New York and the various camera dead zones. One area in a dead zone is the Red Hook Marine Terminal, a port the government blocks out from surveillance. They figure that Decima took Grace there, and Reese spots a delivery truck and realizes how they can get back into NYC.
Grace wakes up in the warehouse and Greer comes in to talk with her. She reluctantly sits down and Greer asks who she is.
Posing as a delivery driver, Reese drives a stolen delivery truck to the terminal. Root and Sam get out of the back and Root hands out walkie-talkies that Samaritan can't monitor. They check the shipping office and discover that there is an extra ship in the harbor, and Root sends Sam and Reese in. They check the ship and discover that Decima has killed the crew using botulinum toxin in a poison bottle of champagne that the company gave them for a job well done. Root calls them back and shows them a cargo container holding sixty state-of-the-art computer servers. She explains that Decima will use the servers to boost Samaritan's abilities, just as they hear someone moving among the containers. Reese shoots, killing the man and hitting the tablet in his jacket. Root hooks it up to the computer in the office and confirms that Decima is involved, and pinpoints the building in NYC where they're operating out of. She tells Reese and Sam to rescue Grant because the Machine has something else for her to do.
Greer reviews Grace's file, explaining that he's trying to learn about her life. She finally mentions that she was engaged to a man named Harold who died in a ferry bombing four years ago, and his remains were lost at sea. Realizing who Harold is, Greer asks Grace if she was able to independently confirm anything that Harold said about himself, and Grace, angry, stands up and says that she's done answering his questions. She insists that she learned how to spot lies because she had an alcoholic father, and she knows Harold would never lie to her or break her trust. Greer, watching her, realizes that she truly loved Howard, and Grace insists that Harold would have done anything for her. Grace asks why he's so interested in Howard, but Greer ignores her and leaves.
Back at the computers, Greer contacts Zachary, who tells him that they're moving in on Reese's car. However, when they surround it, they discover that Reese has paid a homeless man to drive it away. Greer realizes that it's a distraction designed to draw Zachary and his people away from his location, and tells Virgil to pack everything up.
Reese and Sam hide in the trunk of a taxi and pay the driver to take them to the warehouse. They go in and find Virgil still packing, and capture him. Sam confirms that they just missed Grace, just as Greer contacts them on the video screen and assures them that Grace is quite safe with him. Reese threatens to shoot Virgil, and Greer tells him that Virgil is already dead. Getting the message, Virgil grabs Reese's gun, shoves it against his chest, and pulls the trigger, killing himself. Greer tells Reese and Sam to have them bring Finch to the Jefferson Bridge at 6 a.m. and he'll trade them Grace for Finch.
As they leave the warehouse, Reese and Sam wonder what to do next. A nearby payphone ring and Reese answers it. It's Root, who tells them that the surveillance camera across from Grace's building has gone out. Realizing what it means, Reese and Sam drive there and find Finch sitting on Grace's doorstep. He tells them that he took out the surveillance camera and discovered that Grace is gone. Finch realizes that Decima wants him in return for Grace and agrees to do so. He asks Reese and Sam to stay with him and make sure that Decima keeps its end of the bargain. Reese promises to do whatever he asks and Finch asks them to avoid violence if at all possible. However, if Decima harms Grace, he tells Sam and Reese to kill them all.
The next morning, the team take Finch to the bridge. Sam and Fusco stay back while Reese takes Finch to one side. When Reese says that they've faced worse, Finch says that they haven't faced anything worse and that he knew all along that he was tied to the Machine, putting everyone he ever knew into danger. Zachary and his men pull up at the other side of the bridge and get a blindfolded Grace out, and Finch gives Reese an envelope for Grace once she's safe. Reese promises that they'll rescue him, but Finch says that Grace is the only thing that matters. Finch starts walking across the bridge and Zachary sends Grace across from his side. As she passes Finch, she stumbles and he catches her without her knowing who he is. She thanks him and keeps walking, and Finch gets to the other end. As Zachary and his men take him toward their SUVs, Finch looks back and confirms that Grace is safe. Sam and Reese can only watch as the Decima operatives drive away with Finch.
Fusco takes grace back to her house and she wonders if she'll be safe there. Reese arrives and tells her that they'll be coming for her, and gives her Finch's envelope. Inside is a complete set of fake identity papers, and Reese tells Grace that she's got the job in Italy. As he starts to walk away, Grace asks him if it was all about Harold. Reese tells her that all that matters is that she loved Harold and he loved her back, and keeps walking.
Later, Garrison supervises the arrest of a terrorist who Samaritan provided him with. Greer is with him and Garrison says that they'll be in touch if everything checks out with their prisoner. Once Garrison leaves, Greer tells Zachary that they've lost the NSA feeds but gain something far more valuable.
The 24-hour beta test ends and Samaritan shuts down... for now.
Sam and Reese meets with Root in an alleyway. She tells them that they're not finished yet and shows them a truck that she's hijacked with seven of Samaritan's servers.
Finch is seated in an empty office building when Greer arrives. He thanks Greer for blindfolding Grace so she wouldn't know who he was, and Greer says that he wanted to start on a good footing with Finch. Greer sits down across from Finch and admits that Finch has been a hard man to find.