Finch sits at Reese's bedside, watching his unconscious friend. After awhile, Finch realizes there's nothing else that he can do there and leaves for another appointment.
At the funeral of Joss Carter, her ex-husband Paul and her son Taylor sit near the grave. A great many NYPD officers, including Fusco, have turned out for the ceremony. From a distance, Finch and Sam watch.
Later, Finch walks past a newspaper stand with headlines about Simmons, the corrupt HR cop that is now on the run after killing Carter. A nearby payphone rings and Finch answers it, taking down the new Number. He then goes to the library and decodes the Number... and realizes that it's Simmons'.
Sam makes her way through a series of underworld bars and hideouts, interrogating anyone who might know anything about Simmons' whereabouts.
Simmons buys a fake ID from three lowlifes and pays them off. As the men drive off, Reese rams them with a truck, setting their car on fire. Disregarding the flames, Reese interrogates the man in the back, showing him a photo of Simmons. The man tells him what he can and Reese walks away, leaving him to burn.
In 2010, Finch meets with a therapist after the ferry bombing. He finally admits that he lost his best friend in an accident and that he has no one to comfort him since he broke off his relationship with a woman. Now Finch is reevaluating choices that he's made with his life. The therapist warns him that grief can give a false sense of lucidity, but Finch says that he wants to pay tribute to his friend by doing something radical. In response, the therapist explains that she has been working with survivors of the ferry bombing who feel a sense of survivor's guilt, and they all believe that the explosion was their fault. She tells Finch that he doesn't control who lives or dies and that his guilt will eventually passes. Finch responds by asking if it passes when it really is his fault.
Finch brings Root some food and she notes that he looks tired. He tries to ignore her but as he turns to leave, Root says that she can still help him. Finch tells her that it's too late, but Root says that she can help him save Reese, who is still in trouble. The woman warns Finch that there are bigger problems at hand and that whatever The Machine has been preparing her for is coming soon. Before Finch can respond, his cellphone rings and he steps outside to take the call.
Later, Finch meets with Fusco at the scene of the car crash. The detective informs Finch that witnesses have identified Reese at the crime scene, and warns that a scorched-earth campaign will make it harder for anyone to find Simmons. As to the three men that Reese attack, Fusco confirms that they worked for a forger named Seamus Yorke, and Finch says that they need to find Seamus.
Sam finds someone who might know something and strings him up at an abandoned warehouse. Finch tries to call her and when she ignores his calls, tracks him down in person with Fusco. Sam explains that her prisoner is a crook and that Reese tossed him off a building and broke his legs. She doesn't see a point in stopping Reese, but Finch reminds her that Reese was badly wounded during the shootout with Simmons. Sam reluctantly agrees to help and figures that the only way to find Reese is to locate Simmons. Her prisoner speaks up, saying that Alonzo knows Simmons' escape plan. Fusco admits that the Feds won't give him the location of the safehouse where they're holding Alonzo, but Finch has confirmed that Alonzo's lawyer, Jimmy Ransone, has had contact with his client. The trio heads off, leaving the crook hanging from the rafter.
Sam and Fusco go to Ransone's office but discover that he's dead. Someone has been torturing him using lit cigarettes, but Sam figures that it's too amateurish to be Reese's work. Fusco checks Ransone's surveillance system and confirms that Reese was there and interrogated the lawyer. After Reese left, Russian mobsters came and tortured Ransone, killing him. They figure that the Russians want Alonzo since he turned state's evidence after his capture, and Sam tells Finch that they're only other option now is to talk to Root.
In 2005, a QMI hospital manager interviews Sam, pointing out that she was chewing on an energy bar when she told a family that their father had died in her care. He points out that she took heroic efforts to save the man, but wonders if she really cares if her patients live or die. Sam insists that she does and that the other doctors act the same, but the manager says that they just pretend so they can cope with their feelings, and Sam isn't pretending. When Sam argues that she's a better doctor because she doesn't care, the manager says that she's very gifted, but tells her that she'll never be a doctor because she's a fixer, not a healer.
Back at the library, Finch warns Sam and Fusco that there will be consequences if they free Root. They reluctantly agree and Finch lets Root out. When they get back upstairs with the others, a cellphone rings and Root figures that it's The Machine. She answers and smiles in satisfaction
That night, Sam follows Root's directions and drives the others to Alonzo's location. They approach with the headlights off and Root tells them to stop at a building. She tells Finch to get the first aid kit from the car and Fusco wonders why they should bother listening to her. Root assures him that she's there to help, and drawing on The Machine's resources, describes everything from his pocket change to the fact he was named after a lion at the zoo. She then asks Sam for a gun, and Sam refuses. Root then tells her to turn and shoot, just as a Federal marshal comes running out. Sam kneecaps him and Root tells the others to drag the man inside a nearby building. Once they get inside, Root tells them to look at the window of a hotel across the street. Alonzo looks out through the drapes and Root describes all of the security precautions that the Marshals have taken with the safehouse. Fusco wonders if Reese is there... just as a nearby car blows up.
In 2007, a Specops psychologist evaluates Reese's suitability to join the CIA's special unit. He warns Reese that the men involved have to do terrible things and wonders if Reese can handle it. Reese says that he can and that he will do whatever he's ordered, including killing a terrorist in front of his son. The psychologist points out that Reese lost his father, a military officer, and wonders if he'd have second thoughts about making another man's son an orphan. Reese says that he can and the psychologist apologizes for his harsh treatment. Grim-faced, Reese says that he's been through it before and the psychologist wonders what he's talking about. Reese tells him that he is already working for the special unit, and that his orders are to find out who has been selling the names of their operatives to the Chinese. Drawing a gun, Reese tells the psychologist that he should have just done his job and then shoots him dead.
Several of the Marshals run out to investigate the explosion. They call their superior, Pollack, for air support. He's in the hotel room with Alonzo, and tells his men that he's not calling in air support for a car fire. Down below, the hotel manager complains about the fire just as Reese comes in and kneecaps the Marshal with him.
When the other Marshals return to the lobby doors, they discover that they're locked from the inside. They call Pollack and apprise him of the situation. The lights go out and Alonzo tells him that he can't stop the man who is coming for him.
In the hotel, Reese fights off the pain from his chest wound and plants explosive charges. He then piles a stack of emergency flares in the hallway. When the Marshals come down the hallway, using night-vision goggles, Reese shoots the flares, setting them off and blinding the Marshals. He then knocks them out and sets off the explosives, bringing down the hallway behind him.
When Pollack tries to get Alonzo out, Reese gets the drop on the Marshal knocks him out. He then tells Alonzo to give him Simmons' escape plan. Alonzo refuses to betray his own man, and Reese respects him as a man who keeps his word. However, Reese warns him that he always keeps his word, and tells Alonzo that he's going to kill him in three minutes. The HR boss can make those minutes end painlessly, or he can spend them in agony.
At the lobby door, the Marshals cut through the locks just as Sam arrives and takes them out. Root asks for a gun again and Sam refuses, but Finch notes that Root has had plenty of chances to kill them if she wanted them dead. Sam reluctantly gives her two guns just as more Marshals pull up outside. Following The Machine's directions, Root opens fire on them and cripples them all. She then tells Fusco and Sam to find Reese while she watches for more Marshals.
Alonzo writes Simmons' escape plan on a piece of paper. Reese takes it and prepares to shoot Alonzo, but Finch comes in and reminds his friend that Carter sacrificed everything to bring Alonzo down on legal terms. He tells Reese to shoot if he wants, but not to convince himself that he's dong it for Carter. Reese figures that they should have killed Alonzo in the first place and tries to shoot, but then collapses from his injuries. Finch tells him that their purpose is to save lives and asks Reese to let them help him. Ignoring the pain, Reese aims his gun at Alonzo and pulls the trigger... only to discover that he's out of bullets. Fusco and Sam arrive and Fusco tells them to get Reese out while he makes sure that Alonzo doesn't escape.
As Sam drives Root, Reese, and Finch away, she says that she should be hunting down Simmons. Finch tells her that he's not going to lose another friend and that they have to choose. Root, listening in, tells them that she never claimed that The Machine said Reese was the only one who wanted to kill Simmons.
As the Marshals take Alonzo back into custody, Fusco sees the piece of paper that Reese dropped and picks it up.
In 2005, Fusco meets with a police psychiatrist after he shoots a drug dealer, Jules. Fusco assures the psychiatrist that he's been sleeping fine and that it was a clean shooting. Despite that, the psychiatrist still worries that Fusco is suffering posttraumatic symptoms and that he's seen some cops kill themselves out of guilt. He tells Fusco to get real with him and assures him that everything he says is confidential. At that, Fusco tells him that he deliberately hunted down and shot Jules, who had killed an off-duty rookie cop with a child on the way a year ago. The detective tracked Jules down to a bodega and stepped out, and Jules saw him and knew why he was there. Fusco shot him dead, and tells the psychiatrist that the drug dealer got what he deserved--the "devil's share"--because that's the way the world even things out. Satisfied, Fusco thanks the psychiatrist for letting him unburden himself and walks out.
Simmons goes to a private airfield out side of NYC only to find Fusco waiting for him. Fusco says that he sent the pilot on his way and Simmons dares him to shoot an unarmed man. The detective says that he's been waiting a long time to pay Simmons back, and tosses his gun away. They fight and after a brutal struggle, Fusco finally breaks Simmons' arm and knocks him to the tarmac. Simmons tells Fusco to kill him and get it over with. Disgusted, Fusco tells him that he could have ended up like Simmons: a bottom-feeder turning on other cops for money and power. But he had Carter, who showed him that he could be good again. Carter saved him, and Fusco has no intention of throwing that away on garbage like Simmons. He cuffs Simmons and tells him that he's under arrest.
The next morning, Fusco drags Simmons into the station past the other cops.
At the hospital after the funeral, Finch and Sam check on the unconscious Reese. The doctors have confirmed that Reese will pull through. Sam wonders where Root has gone and Finch goes back to the library. He's surprised to discover that Root is back in the cage, reading a book and petting Bear. When he wonders why she came back, Root explains that they should be together for the big fight when it begins. Finch thanks her for her help and then closes the cage door.
The next night at the hospital, Elias gets into Simmons' room despite police security and sits down next to him. When Simmons wonders why he's there when he's lost, Elias tells him that he liked Carter, and owes her a debt. He admits that she didn't particularly like him, but wouldn't let him kill Simmons for her. Now that she's dead, Elias considers himself under no such restraints. When Simmons asks if he plans to kill him, Elias tells him that he's only going to watch... and has his henchman Scarface garrote Simmons.