Jane and Frankie are seen chasing a suspect through a subway station before we jump back in time a day.
Jane and Maura are discussing Kent Drake, Maura's new potential assistant medical examiner. Jane thinks Drake sounds like a superhero, though Maura continually tries to argue with her. Angela comes in with an ugly chair wrapped in plastic. She says that she bought it for Frankie so she doesn't care if the girls like it or not. Jane and Maura get called to a case and tell Angela they can't help her move the chair to Frankie's right now.
Jane and Maura meet Frankie and Vince at the crime scene. An unidentified woman has been found in a dumpster, wrapped in a rug.
There is a brief conversation about how Frankie is trying for a commander position, and has eaten with every commanding officer except for someone that Vince says nobody wants to watch eat. Maura says the officer in question has a temporal mandibular disorder, making Vince feel bad.
Back to the crime, the body was dumped within the past two days, and it may have taken two people to move it. The team discusses who would have stood out in downtown Boston. Frankie seems annoyed with Vince, Maura and Jane's silly suggestions and leaves.
Maura and Jane meet Kent Drake in the lab. He has already unwrapped the body and organized the personal effects. Jane thinks he is weird, and he returns the feeling. Jane notices the woman had a bag marked Internet Village and goes there with Vince to talk to her co-workers.
A woman identifies the dead woman as "Mona." She hasn't seen her since she gave her notice three weeks ago. Mona had a boyfriend named Spike, which Vince doubts is the guy's legal name. In any case, the co-worker didn't like Spike but didn't want to say anything. She shows a photo of him to Vince and Jane.
Maura and Jane help Angela move the chair into Frankie's apartment. The apartment looks different, and Angela lets it slip that Frankie moved. He didn't want Jane to know. Frankie comes out and is annoyed that everyone is there. Jane is annoyed that Frankie didn't tell her. As he scrambles to put on a shirt, he explains that he wanted the apartment to be nice before he showed it to anyone. He doesn't want the chair and asks them to take it back downstairs while he prepares for a date.
Vince and Jane talk about the investigation. Mona had a packed suitcase, suggesting she was going to run away from Spike. There's no evidence he abused her, as neighbors say they never heard them fighting, though Spike went off on a neighbor who complimented his hair. There also were no rugs in Mona's apartment.
Frankie engages in some banter with Holliday, who then tells him that Mona made a lot of calls to someone named Cecil Wilson.
Maura is showing Drake around. He asks her if she enjoys the managerial side of her job.
Frankie stakes out Cecil Wilson's apartment, and hasn't seen him go in or out. He watches while Vince and Jane go knock on the door. Wilson bolts down a fire escape. Jane tells Frankie via walkie talkie, leading to the chase sequence seen at the beginning of the episode.
Frankie chases the suspect towards a subway that is coming. He pulls out his gun, orders the suspect to drop it and shoots. Vince tells the crowd to back up, revealing that Frankie has shot someone else. Frankie calls for an ambulance. Vince asks him if he saw a gun. He did, but panics when Vince asks him where the gun is, as he doesn't know.
Vince questions Frankie about what happened. He says he was chasing Spike and he saw this other guy with a gun. He gets defensive when Vince asks him if it's possible Spike had the gun. Jane tries to reassure him but he doesn't think they will have time to do their own investigation before IAD gets there. However, Maura says Frankie is anxious and she can administer a sedative--which will also buy them time, as Frankie can't talk to anyone until the sedative wears off. Vince arranges for a union lawyer to meet Frankie at the hospital.
At the hospital, Vince tells Jane that the man Frankie shot was named Sean Hughes. Jane wonders if Sean was working with Spike and that's why he pulled a gun. However, the gun hasn't been recovered, so Vince is skeptical. Their conversation is interrupted by IAD's arrival.
Jane goes to see Holliday on the sly so that they can clear Frankie before IAD talks to him. Holliday says that Sean was a college student who participated in political protests, but was never violent. He did not have a license for a gun. Tech is sweeping the subway platform for the gun. IAD calls and wants to meet with Jane. She makes an appointment for half an hour.
Maura receives the contents from Mona's stomach. She appears to have ingested a protein shake. Computer geeks often drink it to ensure they don't have to get up from their chairs to eat, but Mona's muscle tone suggests that is not why she drank it.
IAD interviews Jane and wants to know how Frankie seemed. She asks why they don't just look at the security tape. IAD knows something but won't tell her. Later, Sam Lewis slips Vince a note informing him the subway camera was broken so there's no proof of what happened. Vince tells Jane that Frankie will be held responsible for the shooting as a result.
Angela doesn't let Frankie watch news about his case. Frankie worries he might go to jail, but Angela believes in him and also believes Jane won't rest until she gets to the bottom of it.
Sean Hughes dies and his body is brought in for autopsy. Maura and Jane can't participate because of their relationship to Frankie. So Maura sets up a video link for them to watch it from another room. The medical examiner is blocking their view of his report on the stomach contents. Maura gets him out of the way by taking Jane's coffee into the autopsy room and leaving it on a table for him. They see that Sean had ingested a similar protein drink to Mona. Jane calls Vince and asks him to call in a favor with a judge so that she can use this as evidence that Sean and Mona were connected somehow and thus investigate the shooting as part of her investigation into Mona's death.
Vince and Jane go to an apartment, where a cop is guarding the door and doesn't want to let them in. They offer to put in a good word with his sergeant for him because he is so dedicated and go in anyway. They find a bunch of routers. Jane sends Holliday a photo. Holliday says the routers are broadcasting from all over. She asks them to come back to the station. She's found some social media videos of the shooting, and they clearly see that Sean Hughes had a gun, and that someone took it between when he was shot and when Frankie checked his pulse. They decide not to tell IAD until they have another suspect in mind.
Jane and Vince review the video. Jane notices a guy in the background who doesn't appear to get upset when Frankie shoots Sean. Maura runs facial recognition software on this person while Vince meets Drake and doesn't like him. Facial recognition identifies the guy as John Stanton, a political protestor whose house was seized by the Boston Rapid Transit Authority to make room for more public transportation.
Vince and Holliday return to Sean's apartment. The same cop doesn't want to let them in even though they have a warrant and Vince suggests he call Internal Affairs to keep himself out of trouble. They only have 15 minutes. Holliday says someone is pinging the routers to find out where they are.
Jane shares the good news with Frankie and Angela. Frankie is grateful and bear hugs her until Vince calls her back to work. They go to a cafe where presumably they will find Stanton. Jane offers to let Vince stay in the car so that IAD won't be angry at him. He's not interested. He knocks on the cafe door and comes face to face with Spike.
Vince and Jane questions Spike, who claims he didn't know how Mona died. Jane tells him that they know about the connection between him, Stanton and Sean and they also know Stanton wants to mess with the subway system and possibly cause a crash. Since Sean is dead, Spike will be on the hook when Stanton's plan goes into action.
Jane shows the video of the shooting to IAD but they are unimpressed and think it proves nothing. She tells them about their theory that Sean, Spike and Stanton were trying to cause a subway crash at the time of the shooting. IAD wants proof. They bring in Spike and he admits that Sean had a gun. Jane will give IAD credit for solving the case if they drop all charges against Frankie.
Maura finds a melancholy Drake looking at Mona's body. Drake asks her if solving the case makes her feel better about the fact that someone was murdered. She tells him that most of the time, learning the truth helps the people who loved a murder victim. Later, he dresses up to go out for the evening and Maura is impressed. He admits he dresses like a nerd to see how people will treat him.
The gang celebrates at Frankie's new apartment. Frankie buys them all presents to thank them for their help. He admits to Jane that he feels terrible that Sean died because he didn't want to kill anyone. Jane assures him that that means he's one of the good guys.