Fusco drags Detective Still's corpse into the woods. Sobbing, he puts it into a grave.
An informant calls and offers to tell the police everything they want to know about Fusco and his connection to HR.
Reese is posing as a waiter an award ceremony at the Booker University Medical Center as Dr. Juliana De Matteo introduces their guest of honor, cardiologist Dr. Richard Nelson. As Reese watches their new Number as he receives a professor emeritus, his daughter Molly sits at the bar, drinking champagne. Richard notices her and hesitates momentarily as he recognizes her.
At Cal's funeral, Quinn is giving the eulogy. Among the mourners is Fusco, who watches Simmons. Carter is seated nearby.
Molly walks out and Nelson starts to go after her. One of his patients, a hedge fund financier named, Brandon Boyd, stops him. Brandon wants to talk about health care financing and they make a racquetball date. Once he leaves, Dr. Garrett Rossmore offers Nelson a bottle of rare whiskey compliments of a patient that Nelson helped. Nelson apologizes for the board's decision on his drug trials, and Rossmore admits that the data wasn't there to support his theory. Finch informs Reese that Rossmore now works at Philia Pharmaceuticals, and the board's decision cost Philia millions in revenue.
After the funeral, Fusco approaches Simmons and warns him that he knows he had something to do with Cal's death. He promises to take him down, and Simmons reminds him that Fusco no longer has HR protection. Simmons knows that IAB is looking at Fusco's former partner, Azarello, on a dozen murder counts.
Juliana comes over to offer her congratulations to Nelson, and Finch confirms that she's Nelson's protégé. However, she hasn't made tenure. Nelson asks after Molly and Juliana says that she took off early. She notices that Nelson's nose is bleeding and goes to get a napkin. Reese gives him a napkin while Finch checks and confirms that Molly is a junior and was suspended after assaulting a police officer during a campus demonstration. Meanwhile, Nelson drops his champagne glass and Reese goes over to help him. He gets the doctor into a chair and warns Finch that their Number may have been poisoned.
At the station, Detective Joseph Soriano with IAB tells Fusco that they need to talk about the disappearance of Stills. He tells Fusco to hand over his badge and his gun and Fusco reluctantly does so, while Carter watches. Once she gets the chance, she goes into the interrogation room where IAB is holding Fusco. He tells her that it's none of her business but Carter reminds him that she's his partner. Fusco points out that he asked for her help once and she refused, and says that the past is coming back to haunt him. He advises her to stay away from him, while Carter gets a call. She tells Fusco that they're not done and steps outside to take the call. It's Finch, who offers his condolences on Cal's death. She wonders why they couldn't stop the murder in time, and Finch admits that he's not sure why. Finch asks for her help and Carter says that she has other problems. She tells Finch that she needs him to clone a phone for him.
Nelson goes back to his lab and calls Molly. He thanks her for coming, pointing out that the last time they met, she threw red paint at him because his university lab uses animals for medical research. Nelson reminds her that his salary from the university paid for the roof over her head. His nose continues to bleed and he tells Molly that he'll get back to her. Reese watches from across the street as Nelson vomits blood and then checks himself in a silvered tray. The doctor calls 911 and says that someone tried to kill him, and staggers outside. Reese approaches him and Nelson figures that he's involved when he recognizes him from the ceremony. The police pull up in response to the 911 and Reese slips away while Nelson tells the officers that someone tried to poison him. Reese calls Finch and warns him that they may already be too late.
Soriano tells Fusco that they've received information on Stills' disappearance. Fusco explains that they worked a beat coming up but they went into separate divisions.
Fusco is drinking at a bar and the bartender finally orders him out. Stills offers to take him home and Fusco tells him that his wife filed for divorce and full custody of their son. Fusco's partner offers to put him up at his place and Fusco takes him up on his offer.
Finch goes to Nelson's lab and scans for low-level alpha particles. Reese figures that it's polonium, and only lethal when ingested. The substance is fatal if not treated in the first hour. Reese checks on Nelson at the hospital and tells the doctor that he's there to help. However, he admits that he's too late and tells Nelson that he's been poisoned with polonium. Nelson has less than 24 hours to live and Reese suggests that the doctor come with him and find out who killed him.
Reese tells Nelson that first he has to get his affairs in order. Nelson goes to see Molly, who is handing out protest flyers. She figures that he's there to chew her out, but Nelson says that he's there to see if everything is going okay for her. He hesitates and then apologizes for not being more involved in her life. Molly wonders why he's there and reminds him that he cheated on his wife, and Nelson says that he's made a lot of mistakes but having a daughter wasn't one of them. He tells her that he's proud of her and Molly says that she'll call him tomorrow.
Carter listens in as Soriano explains that Stills and Azarello had a man on the inside with Homicide. The IAB man has video of Azarello explaining how Fusco helped him and Stills out. Fusco says that Azarello is lying but Soriano has the prisoner's full confession on video with details about the first time Fusco helped them.
Stills calls Fusco to a tenement and shows him a dealer that they had to shoot when he wouldn't play along. Fusco realizes that they want him to cover for them, and Stills reminds him that he's always had Fusco's back. He asks Fusco to help as a friend and Fusco finally tells them how to clean up the crime scene.
Carter goes to see Azarello and asks why he's suddenly talking to IAB when he's been in jail for over a year. Azarello asks why she hasn't been interested in Fusco's past until now, but she asks if HR is responsible. The prisoner takes the photo of Stills and says that sometimes the past comes back to haunt people. Carter offers him a deal with the DA, but Azarello says that she's too late to make a deal and walks off.
Finch checks in with Carter, who has checked the names of the people close to Nelson. Brandon's company, VAC, is under SEC investigation for insider trading after they dropped Philia's stock. Finch relays the information to Reese, who has Nelson confirm that Brandon's company handles his stocks. Reese confirms that Nelson told Brandon about the failed drug trials, and explains that Brandon made $500 million from his inadvertent tip. The SEC doesn't know the insider and Reese figures that VAC plans to eliminate the weak link. Nelson finally admits that he screwed up and now he's dead, and Reese assures him that he doesn't deserve to die. The doctor says that he needs to talk to Brandon.
When Finch goes back to the banquet hall where the ceremony was held, he confirms that the water at the podium was poisoned. Reese and a waitress were the only two people who had access, and Reese knows who hired the waitress.
Brandon is leaving a club when Reese pretends to be a valet, knocks him out, and gets him into his car. Nelson is in the back and Reese drives away in the car. Once Brandon wakes up, Nelson takes a gun from Reese and demands answers. Brandon apparently has no idea that someone has poisoned Nelson. When Nelson fires a shot into the car door, Brandon explains that he needed an edge to keep his job, and his boss Vincent Cochran wanted results. However, he insists that he didn't know anything about a poison attempt. Brandon admits that he told Vincent about Nelson, and Vincent said that he would take care of it. When Nelson fires another shot, Brandon tells them where they can find Vincent, at an upstate lodge.
At the station, Soriano tells Fusco that he knows that the detective was doing more than just covering for Stills and Azarello.
Stills calls Fusco to another drug bust gone bad. When Fusco tries to walk, Stills tells him that it's too late. A dealer charges out of the next room and Fusco instinctively draws and shoots. Stills tells Fusco that he knew he was solid, gives him some money, and welcomes him to the crew.
Soriano tells Fusco that Azarello flipped on him. They checked the car that Fusco signed out on the day that Stills disappeared, and found bleach stains in the trunk. Soriano figures that Fusco wiped it down to eliminate DNA evidence, and shows him phone records showing that Fusco was in Oyster Bay at 2 a.m. on the night that Stills disappeared. The IAB officer also has satellite photos showing disturbed ground in the area where Fusco made the call, and tells him that in the morning he'll move units in to search the area. Meanwhile, Carter listens in on the entire conversation.
Fusco goes to the restroom and finds Carter waiting for him per his request. He tells her that he didn't kill Stills but he'll go down for it anyway. Fusco admits that he deserves it because of the other bad things that he did. At first he thought he was cleaning up the streets and taking drug money from dealers. Still was like a brother to him and when he asked for help, Fusco eventually got roped in. Fusco tells his partner that he was a dirty cop, but things have changed since he met Reese and Finch. He just wants Carter to understand, but Carter tells him to stop and says that she doesn't know who he is anymore.
Reese and Nelson drive upstate with Brandon, and the doctor says that it's time to face the consequences of his mistakes. He passes out and Reese pulls over and tries to revive him with a shot of adrenalin. Nelson wakes up and Reese tells him that he has one more mission to finish before he dies. He gets Nelson into the car and then punches Brandon unconscious and leaves him lying on the side of the road.
A short time later, Nelson walks into the lodge's lounge and sits down next to Vincent. Vincent doesn't recognize him and Nelson says that he's the man that Vincent murdered.
Carter finally calls Reese and asks what he's doing about Fusco. As Reese searches through the lodge's uniform rack, he says that he isn't doing anything and points out that Fusco is her partner. She asks if he knows what Fusco has done, and figures that he deserves to be behind bars. Reese tells her that she'll have to make the call herself, and that in the past she's always figured that a dirty cop is always dirty. He hangs up, leaving Carter to consider what to do next.
Nelson describes the effects of polonium on the human body, and then figures that Vincent's company has no interest in medical research. Vincent says that he had to dump a loser, and in the end he always wins. Nelson admits that he's done a lot of bad things and he's ruined his life, but he doesn't deserve to die. When Vincent says that the SEC investigation will die with Nelson, Nelson says that it will die with both of them and points out that Vincent's nose is bleeding. Vincent looks up and realizes that Reese, dressed as a servant, served him his wine. Nelson tells him that he has 24 hours to spend his billions and advises him to spend it wisely.
The next morning, Soriano drives Fusco out to Oyster Bay where the search teams are going to work. He tells Fusco that nobody gives a crap about him and they head off.
Nelson calls Molly and they chat about the boyfriend who dumped her, and then says goodbye. Reese brings him a drink of his favorite whiskey, and Nelson thanks him for giving him another shot. He dies a few seconds later and Reese tells Finch that they've lost their Number. They both wonder why they arrived too late again, and Reese asks if there's something wrong with The Machine... and who else they're missing.
Simmons accompanies Fusco and Soriano and whispers to Fusco that he's as good as dead. The dogs find a scent but the officer tells Soriano that while there was a body there, someone has moved it. Soriano tells Fusco that he knows he killed Stills and promises to hang it on him. Fusco tells him that he's not a dirty cop and walks away.
When Reese returns to the library, Finch informs him that Fusco is off the hook. Finch has talked with Elias, who has made sure that Azarello recanted his testimony. He tells Reese that the storm he mentioned some time back has arrived, and checks a monitor showing the progress of the virus that Kara planted. Reese notices that Bear is gone, and Finch tells him that there is another matter they need to discuss.
At the station, Fusco collects his gun and badge. Carter comes over and gives him a file to look at for her. She says that she had a long night and leaves with Bear... both of their feet covered with dirt. In the file, Fusco finds the information she has on Cal's murder. Meanwhile, The Machine continues observing but suffers from signal corruption, forcing it to shut down its primary systems.