A man on the phone says that people used to understand things like dignity and respect, and tells the man at the other end to take care of it.
Reese is across the street from a recently remodeled restaurant, Grand, watching the newest Number, Riley Cavanaugh. He works for racketeer Graham Massey and Massey's son Eddie. Riley has no living family and a high school education. All he's done is drive a truck for Massey for the last several years. Reese decides to go in and sits at a nearby table and clones Riley's phone. The hostess, Annie Delaney, tells him that his server will be there shortly and the owner comes over to check on George. They chat and George tells the owner, Al, to pay up. When Al asks for more time, George isn't impressed and tells him to pay up right away. Eddie flashes a gun and says that the next time he'll come by to collect.
George calls Annie over and asks if she's found somebody. She reminds him that her husband, Sean, was one of his and died and George admits that it's tragic but Sean worked with the Russians. When Annie points out that Sean worked for him, George reminds her that Sean was a gambler and got in too deep. He tells her to accept it but Annie says that Sean was a sweet guy until he started working for George. She asks who will miss him when he's gone and walks away, and George abruptly leaves with Eddie and Riley. Reese and Finch, listening in, are both impressed.
George and his men go to a bar and Reese follows them. They check their phones at the bar and George goes into the restroom. Finch clones the other phones through Riley's while Reese spills a drink on his jacket and bumps into George, slipping a bug into his jacket. George, offended, tells his men to throw Reese out and then the racketeer goes in the back and complains about Annie's lack of respect. Riley suggests that he pay her a visit and tell her to drop the subject. George agrees but tells him to make Annie disappear. When Riley hesitates, pointing out that it might hurt morale to kill the wife of a mob widow, George tells him to worry about his morale and to take Eddie with him.
That night, Reese follows Eddie and Riley and Finch informs him that Annie was widowed nine months ago when Sean was killed by the Russian mobs before Elias took over. The two enforcers pull up at Annie's apartment and Riley assures Eddie that he'll dispose of the body. George calls Eddie and tells him to take care of Riley first because he didn't come clean. Eddie hesitates and then assures his father that he can handle it. Reese, listening in, realizes that Riley may be the victim after all.
Before he can move in, there are muzzle flashes inside the enforcers' car and it goes out of control. Riley staggers out and calls Annie at her apartment. She knows him and Riley tells him that George must have found out about them. He says that he had to kill Eddie and assures Annie that things will be all right. Riley tells her to go to their place and he'll meet her there soon. Finch and Reese realize that they now have two people to protect.
The next morning, Reese follows Riley and Finch suggests that they should protect Annie but not Riley. He says that Riley is a killer and not worth the risk, but Reese reminds him that he was a killer. When Finch reminds Reese that the police will be looking for Riley for Eddie's murder, Reese calls Carter and sends her to the address where Eddie's body ended up. Meanwhile, Riley goes toward his apartment but spots two of George's men and ducks out of side. Reese and Finch realize that they'll be looking for Annie as well and that someone needs to check on her. Finch hesitates and then says that he'll go there. Reese spots Riley slip away and goes after him, while Finch tells Bear that he'll be fine.
Carter goes to the crime scene and finds her friend, Detective Szymanski, covering the crime scene. They look at Eddie's body and figure the shooter was in the car. They find his cell phone with a blocked call and several missed calls after that that they figure were from George.
Finch goes to Annie's apartment and confirms that she's gone. He looks around the apartment and finds a desktop photo of the New York City landscape. Meanwhile, Reese follows Riley but loses him when he's forced to duck back.
Szymanski takes Carter to George's bar and introduces her to the racketeer. They inform him about Eddie's death but he already knows about it and doesn't seem particularly concerned. When Carter calls him on it, George assures her that she'll see his feelings when they find the killer. She asks him who made the blocked call but George tells her to focus on the killer. Carter notices that none of his men are there and figures that they're out looking for the killer and George already knows who it is. He tells her that she'll never know if he finds the killer. As they go, Fusco sits at the bar and drinks, and overhears George call and tell his men that he wants to know as soon as Riley and Annie turn up.
Finch goes back to the library and measures the angles of the photo to determine where it was taken. The address is Riley's first home, four blocks from Reese's current location. Reese gets there and finds Riley and Annie on the roof. He's saying that he wants to get her out of town alone but she refuses to go without him. Annie reminds him that he gave her his number after Sean was dead and promised to be there for her, and when she called about a broken water heater he came to help. She insists that she needs to know she can count on him.
Eddie agrees to leave with her and he takes a duffel bag from an air vent. However, he discovers that it's empty except for a cell phone. The phone rings--it's George, who tells Riley that he knows about his stash. George's men come out and open fire, and Reese takes them out from behind while Annie and Riley run downstairs. Reese goes after them and finds Riley waiting for him. He shoots Reese and then leaves, but Finch is okay because of his bulletproof shirt. However, by the time he gets to the street, Riley and Annie have escaped.
Carter and Szymanski get a call that the fingerprints in the car belong to Riley and get the call about the shooting at Riley's home. They figure Riley is the killer and George is looking for him.
At George' bar, Fusco continues drinking and watches as George's men come in to see their boss.
Reese goes to the library and Finch wonders if he's reconsidering his decision to protect him. He goes back to trying to locate Annie and Riley, while Fusco calls to tell Reese that he's overheard George putting out a million-dollar contract on the couple. Once Finch cuts off, he warns that every hired gun in the city will be looking for them. However, they figure that George is too small-fry to do it on his own and that he will reach out to someone, and they both know who. While Finch goes to check out their hunch, Reese figures he knows where Riley is going to get money.
As Reese goes back to Grand, Carter calls and asks why he's protecting Riley. Reese explains what is going on and Carter warns him that Szymanski plans to bring in Riley one way or another. She's less than thrilled when Reese tells her to keep Szymanski away from Riley. Meanwhile, Reese spots Anne and Riley going into the restaurant. She borrows all the money Al can spare and he warns her that George's men came by earlier, asking for her. Al notices Riley and asks if Annie is okay and she assures him that she is.
Reese spots two hired guns moving in to collect the bounty. Riley spots them as well and gets out the back with Annie. When the two men follow the couple, Reese is waiting and takes them out. He checks in with Finch, who is at the prison meeting with Elias. Finch points out that Reese saved Charlie Burton and Elias realizes that he's dealing with Reese's employer. The mobster thanks Finch for saving his life and Finch points out that he still controls the city's underworld. Elias complains he has nothing to do in prison and he can't find a decent chess partner, and asks why Finch is there. Finch explains that they need help with George. They have Riley under his protection and Elias dismisses George, saying that the people lurking in the shadows are the ones to watch out for. Finch asks him to withhold his assistance if George asks for it and Elias agrees... for a price.
Riley and Annie go to the train station and Riley has her stay put while he gets train tickets. Reese follows them in and Finch calls to tell him that Elias has ordered everyone to stay away from the couple. One killer, Ochoa, moves in and Reese spots him, but the bounty hunter backs away when two policemen move in on Riley. Ochoa starts a fire to distract the cops and abducts Annie. Riley runs after Ochoa and Reese runs after both of them. When Finch wonders why Reese is protecting a killer, he inadvertently blurts out that Riley is bad code. Reese doesn't know what he means and Finch tells him to forget it. As he heads for his car, Reese explains that Riley is going to find George before Ochoa delivers Annie to the racketeers. Meanwhile, Fusco calls Finch and tells him that George slipped out the back.
Reese grabs Riley and pulls him into an alley. After a brief fight, Reese takes Riley down and says that he knows what Riley has been doing to protect Annie. Reese also points out that the Russians wouldn't have killed Sean when he still owes money and then left the body in their own territory. Riley lunges at him and Reese pins him to the wall, and the enforcer explains that Sean was skimming from George to pay the Russians back. Reese figures that Riley is right... but that he was the one who made the hit on Sean. Riley says that George assigned him to watch Annie to make sure that she didn't ask too many questions, but he fell for her instead. Reese warns him that he can't run away from what he's done, and Riley says that he knows what he is and he'll do whatever he can to save her. After a moment, Reese gives Riley his gun back and warns him that he can't go half-cocked.
As Reese and Riley head down the street, a police car moves in and they hide between a dumpster in an alleyway. Reese calls Carter, who realizes that Reese is with Riley. He tells Carter that it's about saving Annie and that he'll turn Riley in himself if he's wrong. Carter considers what he's saying and then gives Szymanski a false tip about a sighting. The police car in the alleyway leaves and Finch tells Reese that George has left. Riley realizes that George is heading for a nightclub, The Emerald Pearl, that he uses to dispose of bodies.
That night at The Pearl, George meets with Ochoa. He turns Annie over to George and says that Riley ran for it. Ochoa asks for his money and settles for half. Meanwhile, Reese brings Riley to the door to the club and says he wants his reward.
Inside, George condemns Annie for causing trouble and explains that he had Sean killed for stealing from him. The racketeer says that Riley knows what really happened to Sean. Before he can explain, an armed Riley comes in, threatening to shoot anyone who moves. George is glad to see him and starts to tell Annie about Riley's part in Sean's murder. Reese comes in to back up Riley and a gunfight breaks out. Riley gets Annie to cover and tells Reese to get her to the kitchen because he's closer. Annie refuses to go without Riley but he tells her that it's okay. She reluctantly goes with Reese and one of the thugs shoots Riley in the chest. George comes over and says that he should have killed Riley himself, and Riley echoes Annie's words earlier that no one will miss either one of them. They both fire, hitting each other.
Finch pulls up outside and Reese gets her into the car and then goes back for Riley. When he comes in, he discovers that the bounty hunter killed Riley and escaped. Reese finds a train ticket on the enforcer's body and leaves.
Later, Reese takes Annie to the train station and gives her the single ticket. She realizes that Riley wasn't going to go with her and Reese says that the triggerman knew that he'd have to stay behind. Annie admits that she was fooling herself into thinking that she could change him, but Reese assures her that Riley said that she was the best thing that ever happened to him. As she leaves for New Mexico, Finch comes in and Reese asks what he meant about "bad code." His partner explains that it applies to machines and that humans can evolve... even a killer. As they go, Reese asks what Elias wanted in return for calling off the bounty.
Finch goes to see Elias and plays chess against him.
As Ochoa prepares to leave town, Reese tracks him to his apartment. He offers Reese the money but Reese just smiles and says that he's not there for the money.