True to form, the episode of Elementary opens with Joan being rudely awakened by one of Sherlock’s antics, namely a cell phone whose ringtone sounds like a screaming girl. Upon answering, Sherlock tells her to come to a crime scene in the Bronx. When she arrives, she immediately notices that it’s a gang murder, not within the realm of Major Case. Sherlock tells her that he heard the case on one of his police scanners, and that one of the men found running from the crime scene matched Joan’s old client Shinwell to a T. In addition to this, Sherlock also points out that a gold cross is hanging from the fence that surrounds the murder scene that looks just like Shinwell’s.
The murdered man is a gang member from the local gang, Los Espectros, named Ricky Morales. Morales was found shot twice at close range with a gun Sherlock figures is a Japanese gun from World War II. Unfortunately, they can’t get ballistics on the gun for another three days, as the lab is currently being cleared of asbestos. Los Espectros is the rival gang to Shinwell’s old gang, SBK, and Sherlock tries to tell Joan that Shinwell has possibly fallen back in with them. Joan refuses to believe him, and proposes that they go to Shinwell’s apartment to see if he is there.
When they arrive, he is not there, his cellphone left behind, his apartment tossed about as if he was in a hurry to leave, and his toolbox that Joan gave him missing. Joan goes to look for his toolbox in one of the local pawn shops, and Sherlock goes to ask some SBK members about what had happened the night before. Sherlock attempts to get the alibis of all the major SBK leaders, to see who couldn’t have possibly done the shooting. However, when he asks directly about the Japanese gun, the gang members tell him he’s done asking questions.
Joan goes back to the brownstone when there is someone at the door, that someone being Shinwell, coming to ask her for help. Joan insists that he call the police, but he asks her to just listen to what he has to say. When Sherlock arrives home, wary of having a suspected criminal he’s not particularly fond of in his home, they listen to Shinwell tell the story of how he is a criminal informant for the FBI, helping them bring down SBK from the inside. On the night of the murder, Shinwell was with the man who killed Morales, and before they could dispose of the body, they heard the police coming, so they ran and Shinwell tossed the gun as he ran. If his prints are found on the gun from the crime scene, he will be found in violation of parole and sent back to jail. To clear Shinwell’s name, Joan says she will go to his handler at the FBI, Agent Whitlock.
Joan goes to the local FBI field office to meet with Agent Whitlock, to see if he will cover for his informant. Whitlock tells her that he kept Shinwell off the books after being burned by a previous informant from a few years prior from the same gang, therefore, if Shinwell’s fingerprints are found on the gun, he will go back to jail.
Back at the brownstone, Joan informs Shinwell of this information, and he freaks out at the betrayal. Sherlock gives Shinwell his options; he can either take the fall, or try and solve who killed Morales with Sherlock to clear his name. Sherlock tells him to take the second option, as he deduced that someone inside of Los Espectros had Morales to manufacture a turf war between them and SBK. If they find out who tried to instigate the turf war, they can clear Shinwell’s name.
While Joan goes to the precinct to go through files to come up with a list of suspects, Sherlock and Shinwell go to Morales’ apartment to search it after his girlfriend leaves. While they stake it out, Sherlock inquires of Shinwell why he was so ready to give up the gang that used to be family prior to him being in jail. Shinwell tells the story of how he used to be so grateful for SBK for giving him everything before he went to jail. However, when he was in jail, he saw the people that he brought in to the gang going to jail, and he realized that the gang didn’t care about any of them. As this revelation comes to light, Morales’ girlfriend leaves the apartment, and when Sherlock and Shinwell inspect the place, they find therapist’s appointments on his calendar and anti-anxiety medication in the cabinet, leading them to find Morales’ therapist.
While in the precinct, the detective from the crime scene tells Joan that the lab was cleared out, and that they were fast tracking the bullets through, which signals to Joan that they have far less time to clear Shinwell’s name than they thought.
At Morales’ therapist’s office, Sherlock and Shinwell try to get her to tell them what Morales was coming to her for, but she only relents when they tell her he’s dead. She reveals that Morales was having panic attacks from being a criminal informant for the FBI, not from fear of being caught, but from the guilt of selling out his friends. It also comes out that Morales’ handler was also Shinwell’s handler, Agent Whitlock.
Back in the brownstone, Sherlock revises his theory, thinking that Whitlock had Morales killed to manufacture the turf war, which Shinwell corroborates by telling the story of how Whitlock was in his apartment when he came home one day, and threatened to kill him if he didn’t get him better information. The gun from the crime scene is also found out to belong to Whitlock, as his grandfather took it from a Japanese solider on the battlefield in World War II. Joan also reveals her findings that Los Espectros couldn’t have killed Morales, as they were being attacked on all sides, so they were keeping a low profile. Shinwell gets a call from a former friend to come meet them on their turf, and Joan tries to warn him that it could be a trap. Shinwell tells him that he’ll take his chances, as they know about his daughter and he doesn’t want her to be hurt, and goes.
When Shinwell gets to the meeting place, he finds out that SBK wants him for a job moving money, tipping Shinwell off to the motive Whitlock could have to have Morales killed. Joan goes back to the FBI field office and tells Whitlock that they know his reasoning for keeping his informants off the books and killing Morales; Whitlock uses the informants to find out the best time and places where money is being moved by the gangs, so that he can rob them blind and arrest them. She found one of his friends that was shot at the crime scene as he tried to rob Los Espectros, and will use him to corroborate her theory. She gives him an ultimatum; own up to what he has done, or she’ll tell someone. As she goes back to the brownstone, Whitlock calls her, confesses everything, but tells her that he will let Shinwell take the fall before killing himself.
Joan breaks the news to Shinwell, who resigns himself to his fate, no matter how much Joan tries to offer her help to him. Sherlock goes to the police station to ask Detective Bell about his ex-con artist brother, who has cleaned himself up. He asks if Bell feels that even if his brother went back to jail on a technicality, would he fall back in to his old criminal life, to which Bell says yes.
Sherlock goes to find Shinwell, who is repairing the roof above one of the tenants’ apartments. Sherlock tells him how he wiped Shinwell’s prints from the gun, and that he shouldn’t squander his second second chance.