A man on the phone complains that people used to understand things like dignity and respect. He then tells his listener to take care of things.
Reese is watching their newest Number, Riley Cavanaugh, as he goes to a recently remodeled restaurant, Grand. Riley is there with his boss, George Massey, and Massey's son Eddie. Finch runs a background check and confirms that Riley ash worked for Massey, a racketeer, since graduating high school. Reese gets bored and goes in to the restaurant. He seats himself and clones Riley's phone. The hostess, Annie Delaney, briefly jokes with him about stealing her job. Meanwhile, the owner, Al, goes over to greet Massey and make sure that the food was okay. Massey is initially sociable but soon becomes threatening when he demands the money that Al owes him. Al asks for more time to pay him back but Massey has Eddie flash his gun and tells the owner that he'd better have the money the next time that Eddie comes in.
Reese listens in on the conversation and then keeps listening as Massey calls Annie over and asks if she's found someone since her husband Sean died. Annie reminds the mobster that her husband worked for Massey but Massey says that it was the Russians who killer husband because he gambled with them and got in too deep. Massey tells her to accept what happened but Annie says that her husband was a sweet guy until he joined the Irish mob. She asks Massey who will miss him when he's gone and walks away. Angry, Massey leaves with his son and Riley, while Reese and Finch take in the whole conversation.
The three men go to an Irish bar and Reese watches as they leave their cell phones at the bar so no one can listen in. When Massey comes out of the restroom, Reese "accidentally" bumps into him and plants a bug, and then picks a fight. Eddie and Riley toss Reese out while Finch clones their phones via Riley's. Once Massey goes in back, Reese listens in as the mobster complains about Annie's lack of respect. Riley suggests that he go back and correct her attitude, and Massey asks how he plans to do that. He tells Riley to dispose of Annie for good. When the triggerman points out that it might hurt morale, Massey tells him to watch out for his morale and sends Eddie with him.
That night, Reese follows the two mobsters while Finch checks and confirms that Sean was murdered by the Russian mobs nine months ago, before Carl Elias took over their territory. As Eddie drives to Annie's apartment, Massey calls to privately tell his son to take care of Riley first because he didn't come clean earlier. When Eddie hesitates, his father asks him if he can do the job and Eddie assures him that he can. Reese, listening in, realizes that Riley may be the victim of a violent crime, not a cause.
As Reese drives behind the car, he sees muzzle flashes and it crashes into the sidewalk. Riley staggers out and then calls Annie at her apartment, waking her up. He tells her that Massey must have found out that they're involved and that he had to kill Annie. She wonders what will happen and Riley assures her that everything will be okay and that she should meet him at their special place, while Finch and Reese realize that they now have to protect two people.
Reese follows Riley throughout the night and Finch suggests that they track down Annie and ignore the triggerman. He points out that as a killer, Riley isn't worth protecting. Reese points out that he used to be a killer and then calls Carter. He gives her the address where Riley killed Eddie and has her look into it. Meanwhile, Riley goes to his apartment and spots two of Massey's men watching the place. The triggerman ducks back before they can spot him. Reese and Finch figure that Massey will send men to Annie's apartment as well and that someone has to go there. Finch reluctantly says that he'll go and Reese continues following Riley.
Carter goes to the crime scene and greets Detective Szymanski, who was wounded during Elias' coup attempt. They go over the crime scene and figure that Eddie's killer was in the car with him, and find his cell phone. The last call on it that went through has a blocked number and there have been several calls since then that they figure came from Massey.
Finch breaks into Annie's apartment and tries to find out where she might have gone to meet Riley. He finds a computer with a wallpaper photo of New York and takes it with him, while Reese looses Riley in the street traffic.
Szymanski and Carter go to see Massey at his bar. He already knows about his son's death and Carter points out that he isn't particularly concerned. He tells her that he'll see her feelings when they find the killer. Massey ignores her inquiries about the blocked call and tells her to focus on finding the killer, but Carter points out that Massey's men are gone and figure they're already out looking for the killer and Massey knows who it is. He refuses to answer, only saying that she'll never know if he finds the killer. As they leave, Carter goes past Fusco, who is at the bar and listening in as Massey calls his men. The racketeer calls to tell his men to inform him when they find Riley and Annie.
Back at the library, Finch calculates the location where the desktop photo was taken from the camera angles, and confirms that the address is Riley's first home. Reese gets there and finds Annie and Riley on the roof. He secretly listens as Riley tells Annie to leave town without him. She refuses to go without him and reminds him of how he's been there for him ever since Sean died. Eddie agrees to leave with her and takes out a duffel bag that he hid with money. However, he discovers that the bag is empty except for a cell phone. Massey calls him on it and says that he knew about Riley's secret stash. The racketeer's men run out onto the roof and open fire, and Reese takes them down while Riley takes Annie down the stairs. When Reese goes after them, Riley turns and shoots him in the chest. Reese has a bulletproof vest and survives the shot, but he loses them by the time he can get to the street.
Carter and Szymanski get confirmation that Riley was in the car with Eddie and then hear about the gunmen at Riley's old apartment. They both figure that Riley is Eddie's killer and Szymanski vows to take him down.
At Massey's bar, Fusco continues pretending to drink and keeps track of Massey as he meets with his men.
Reese meets with Finch at the library and Finch again suggests that Riley isn't worth protecting. As Reese goes out to locate Riley and Annie, Fusco calls to tell them that Massey has put out a million-dollar bounty on Annie and Riley. They figure that Massey can't put out that much on his own and that he reached out to someone higher up to put together the hunt. Reese and Finch both realize who is responsible and Finch goes to meet with him while Reese realizes where Riley and Annie will go to get money and heads back to Grand.
While Reese watches Grand, Carter calls him and realizes that he's protecting Riley. She warns him that Szymanski plans to bring in Riley, dead or alive, and Reese tells her to keep the detective away from Riley. Annie and Riley go into the restaurant and Reese watches as she borrows as much money as she can from Al. The owner warns her that Massey's men came looking for her earlier, and he wonders if she is okay.
Reese spots two thugs moving in to collect the bounty and goes around the back. Riley spots them as well and takes Annie out the back. They unwittingly run past Reese, who disposes of the thugs and then checks with Finch. Finch is at the prison and meeting with... Carl Elias. Elias is interested to see the man that Reese works for, and Finch reminds him that Reese saved Elias' life when he was posing as Charlie Burton. Elias concedes the point and Finch points out that he is still controlling the city's underworld from prison. The crime boss explains that he's had a lot to do in prison and has been bored because there aren't any decent chess players. Finch says that they're protecting Riley and that they want Elias to overrule Massey and shut down the bounty hunters. Elias dismisses Massey as an out-of-touch old-school mobster and considers helping, but tells Finch that he will have to pay a price for his assistance.
Riley takes Annie to the train station and he goes ahead to get train tickets. As Reese follows them, Finch calls to tell him that Elias has agreed to put the couple under his protection. However, one killer, Ochoa, is going for the bounty anyway. Reese spots him while two cops spot Riley and approach him. Ochoa sets a fire to cause a distraction and then escapes with Annie. Riley and Reese both go after him. Finch, listening in, dismisses Riley as bad code. When Reese wonders what he means, Finch avoids the question. Reese figure that Riley is going to get to Massey before Ochoa can deliver Annie to the mobster. Meanwhile, Fusco calls Finch and warns him that he lost Massey when the racketeer slipped out the back of his bar.
Reese grabs Riley and drags him into an alleyway. The triggerman attacks him but Reese subdues him and explains that he's there to protect him and Annie. Reese suggests that the Russians wouldn't have killed Sean over a gambling debt and left his body in their territory. Realizing that Reese has figured it out, Riley explains that Sean was skimming from Massey to pay back his gambling debts to the Russians. Massey sent someone to take out Sean... and Reese points out that Riley was the killer. Riley tells him that after Sean's murder, Massey assigned him to watch over Annie to make sure she kept her mouth shut, but he fell in love with her. Reese tells the triggerman that he can't run from what he's done, and Riley says that he doesn't plan to and that he'll do whatever he can to save Annie. Nodding, Reese gives Riley his gun back and says that they need a plan.
As Reese and Riley move off, a police car closes in on them. They hide behind a dumpster and Reese calls Carter and explains about how they're trying to Annie. When Carter wonders what happens if Reese is wrong about Riley, Reese promises to take Riley in himself. Carter reluctantly gives Szymanski a fake report about a sighting on Riley and Szymanski pulls his men away from the alleyway. Finch tells Riley that Massey is on the move and they figure that he's heading to the nightclub, The Emerald Pearl, which he uses as cover to dispose of bodies.
As night falls, Ochoa brings Annie to the Pearl and turns him over to Massey. The bounty hunter says that Riley ran and Massey dismisses his former triggerman as a coward. Meanwhile, Reese turns up outside with Riley in tow and tells the two mobsters on duty that he's there to collect the bounty.
Inside, Massey tells Annie that he had Sean killed for skimming and that Riley knows what really happened to Sean. Before he can give her the full stories, Riley comes in with a gun and threatens to shoot them if they move. Massey just smirks and starts to tell Annie who killed her husband, but Reese comes in behind them. The thugs go for their guns and a firefight breaks out. Riley grabs Annie and takes cover, and tells Reese to get Annie out through the kitchen because Reese is closer. Annie refuses to leave without her lover but Riley tells her that he'll be right behind them. She reluctantly goes with Reese, unaware that one of the thugs hits Riley. Massey comes over and admits that he should have killed Riley himself, and Riley asks him who will miss either one of them. They both fire at the same time.
Finch arrives outside and Reese gets him into the car and has Finch drive away with her. He goes back just in time to see Ochoa kill Riley and escape. When he checks Riley's body, Reese finds one train ticket on the enforcer's body and leaves.
Later, Reese takes Annie to the train station and gives her the ticket from Riley's body. She realizes that since he only bought a single ticket, he never planned to leave town with her. Reese says that Riley knew he couldn't go with herself and Annie blames herself, figuring that she was fooling herself for believing that she could change the enforcer. Reese tells her what Riley said about Annie being the best thing that happened to him. As Annie goes to catch her train, Finch arrives and Reese asks about his earlier comment concerning "bad code." Finch tells him that it returns to defective programming in machines, but that he's realized that it doesn't apply to humans and that even a killer can evolve. As they leave, Reese wonders what Elias wanted as payment for his favor.
Finch goes to the prison later and plays chess with Elias to pay off his debt.
Ochoa is preparing to leave town with the money he got from turning in Annie. As he goes, he finds Reese at his doorstep. He offers Reese the money but Reese says that it's not about the money.