Monk is preparing breakfast and squaring his pancakes while watching a news report on a prison breakout of Joe Endicott, who killed a woman and fleeing the scene. He hears the sound of breaking glass in the next room and goes to get his gun out of its case. Joe enters the apartment and Monk clubs him on the head with the case, Monk starts to call the phone and Joe says he shouldn't: he's his brother.
"Joe" explains that he's Jack Jr., Monk's half-brother, and is surprised their mutual father never said anything about him. Monk is skeptical and Jack Jr. insists that he questioning him about their dad. Jack Jr. knows everything about Jack Monk and Monk has no choice but to accept his story. Jack explains that he was using the name Joe Endicott when he was arrested for selling stolen cars. He admits he broke out of prison but swears he didn't kill anyone. Monk starts to call the police again but Jack says he needs Monk's help to prove he didn't kill the woman. He claims the woman was already dead when he found her in the parking lot. Monk is more interested in learning that Jack climbed through the sewers to escape. A shower and a shave later, Monk insists that Jack turn himself in but Jack refuses to go back to jail and asks about Ambrose. He explains that the dead woman, Lindsey Bishop, was a social worker and everyone in prison loved her. If he goes back, he wouldn't last long before someone killed him. He asks Monk to clear his name and promises to go back to prison when he does.
After he changes and eats, Jack explains that he dug his way out of prison through the sewer, came out at 3 a.m., saw a car, opened it and found Lindsey dead. Monk wonders how he managed to dig his way out and Jack notes he didn't have a cellmate. He tried to call 911 but a prison guard opened fire and he ran. Monk doesn't believe in the coincidence and prepares to call the police. Jack appeals to their shared blood but when that fails, he swears to go to prison but asks to call his mother Darlene in Texas first. Monk agrees and Jack makes the call, putting it on loudspeaker. Jack reassures her mother he didn't kill anyone, and she tells him to go to Monk for help. When Jack tells her Monk wants to turn him, Darlene demands to speak to Monk. She appeals to him, saying his father bragged about him all the time. Monk finally agrees
Monk and Jack go to the crime scene where Stottlemeyer and his men are investigating the crime scene. Monk claims Jack is his pen pal but Stottlemeyer notices he's nervous. Randy arrives with the warden while Natalie talks to Jack, who wonders why Monk has a pen pal. Monk notices Lindsey's cell phone wasn't near the phone. The warden, Tom Bennett, says that he takes the murder personally since Lindsey was such a good person. The guard who shot at Jack, Daniel Reese, admits he didn't see Jack attack Lindsey. The murder weapon is an improvised blade made out of sterling silver with the letters GOSF on it. The guards arrive with dogs and they pick up Jack's scent. Jack insists they have to go and Monk quickly leaves with Natalie. They stop at a diner and Jack flirts with the Paraguayan waitress. Monk notices that there was blood in the car but none on Jack's clothing, suggesting he's innocent. Monk wonders who else knew that Jack was trying to escape so that they could frame him. Jack insists nobody knew except his cellmate Shiv. When Monk points out Jack said earlier he didn't have a cellmate, Jack tries to deny his earlier statement but Monk insists he explain. Jack says that Shiv dug most of the tunnel, and then he was moved into Shiv's cell. He knocked out Shiv and used the escape route. Monk insists on going back to the prison to talk to Shiv but Jack says that will reveal their connection.
Monk goes to Lindsey's house and Jack fakes grief to get the superintendent to let them in the house. Monk searches the house while Jack steals coins. Monk is less than thrilled and forces him to put the money back. Jack notices a lot of bad photos and Monk figures that Lindsey wouldn't have put up such poor pictures. Monk realizes they're the discards and someone replaced the original photos with the bad ones. Jack is impressed and suggests they become partners, until Monk reminds him he promised to go back to prison. Back at Monk's apartment that night, Monk tries to sleep while Jack watches movies in the next room. Monk staggers out and notices him reading a book on Paraguay. Monk notices that Jack is watching a movie that their father loved, then starts vacuuming. Once he's done, they enjoy the movie together and Monk asks if Jack was a good father. Jack lets slip that Jack Sr. hasn't been the same since his mother died. Monk notes that he talked to Jack's mother earlier and calls Stottlemeyer.
Jack breaks into tears and apologizes for lying, insisting he's not a killer. Stottlemeyer arrives but before Monk can answer the door, Jack Jr. calls Monk his big brother. Monk opens the door... and tells Stottlemeyer it's a false alarm. Stottlemeyer is surprised that Monk forgot he had a houseguest. He notices Jack is crying, but gives up trying to understand. As he leaves, he tells Monk that Shiv was killed in prison a few hours ago.
The next day, Monk talks to Dr. Bell and mentions a hypothetical case of a prisoner escaping and coming to him. Monk quickly admits it isn't hypothetical and explains how he used to pray that he had a real family. Bell explains it's a fundamental question of what does someone owe their family. Monk mentions Paraguay and how Jack is obsessed about it, and Bell notices that in prison Paraguay is considered the "promised land" because they won't extradite anyone unless they're guilty of murder. Monk goes back to his apartment where Jack is talking to Natalie and hitting her up for (fake) charity donations. He accuses Jack of lying to him again, noting he couldn't leave until Monk cleared his name. Monk explains to Natalie that Jack is his half-brother and Natalie quickly grabs her check back. Monk notices that Jack is wearing a watch from Lindsey's apartment and realizes that he stole it. Jack notes it's a guy's watch and tells them to take it back. As Monk berates his brother, he notices something on the watch and Natalie explains to Jack that Monk solved the case.
Monk, Natalie, and Jack go to see Reese at his home while Natalie is upset that Monk didn't tell her the truth. Monk shows him the watch and notes that it's engraves to a "DR." Reese notes there are three people at the prison with those initials and insists he has a wife and kid. Monk quickly leaves while whispering to Natalie that Reese is the killer: he has a sterling silver spoon with the same GOSF lettering as the murder weapon. Before they can leave, Reese opens fire on them and they run for cover. Jack has a gun and returns fire, and Monk realizes it's his gun. Monk explains that Reese and Lindsey were having an affair, things went bad, and then helped Shiv escape. Reese killed Lindsey in the parking lot, but ended up framing Jack when Jack "stole" Shiv's escape. Jack runs out of ammo and their cover collapses. They need to get to Natalie's purse to get her cell phone and Jack volunteers. He says that Monk was wrong about him and ask for the car keys. He gets to the car... and drives away. Reese comes after them but Jack returns and rams him with the car. Jack just smiles when Monk wonders why he didn't escape.
Later, Stottlemeyer tells them that Reese has confessed to the DA and Jack will get extra time to his sentence. Jack wants to say goodbye and is glad to hear Monk finally admit they're family. Monk even says he might visit Jack in prison some day. As Jack is taken away, Monk says he's proud of what he did and proud to have Jack as a brother. He even gives Jack a hug of sorts. As Jack is driven away, Randy realizes that his handcuff keys are missing.