On what is supposed to be her last day at work, detective Sarah Linden is called to the scene of a violent crime after a blood-covered woman's sweater is found in a park. There is no body however. The police have also found an ATM card in the name of Stan Larsen. Sarah and her replacement, Stephen Holder, follow-up and when they learn that the Larsen's 17 year-old daughter Rosie did not spend the weekend at a friend's house and has not been seen since Friday night, they suspect the worst. While Rosie's parents Mitch and Stan try to locate her on their own, the police concentrate on searching the park where they eventually discover a car at the bottom of a small lake with the body of a young woman in the trunk. They also learn that the car is registered to the election campaign of city councilman Darren Richmond who is running for mayor.
With Rosie's body now identified, Det. Sarah Linden and Det. Stephen Holder begin the painstaking task of recreating her movements, learning about her circle of friends and tracing her movements after she left the Halloween dance at her high school on Friday night. They question Councilman Darren Richmond who says he has no knowledge as to why Rosie would have been in the trunk of a car registered to his mayoralty campaign. He refuses to play politics with the situation. Linden interviews Jasper Ames whose father interrupts the questioning. At Rosie's school, Holder learns about the cage, a place in the school basement where the kids go for privacy. It may also be the crime scene. The Larsons tell their two boys that their sister is dead.
While the crime scene unit collects evidence in the school basement, Richmond's campaign faces a crisis when news of Rosie's death leaks to the press. He's also found the leaker. He's also scrambling to save his campaign. Linden and holder want to question the school janitor, Lyndon Rosales, who would prefer to jump out a third story window than meet them. He has a pretty good alibi as far as Rosie's death is concerned but he does give hem a new lead, a student named Kris Echols. Mitch Larsen finds herself unable to cope with their loss.
With the video from Rosie's phone, Linden and Holder think they have the killers. It's not that simple however and they soon find themselves back to square one. Linden re-interviews Rosie's BFF, Sterling, and learn that Rosie used to regularly take a bus to a distant part of town. Mayoralty candidate Darren Richmond's campaign is rapidly going downhill and his staff propose a major ad campaign. The only problem is that the campaign needs a infusion of cash. Rosie's parents prepare for her funeral and visit a funeral home to select a casket and go to the church to arrange for the service. Linden decides to again search Rosie's bedroom and finds handwritten notes notes from an interesting source.
Having found Rosie's hidden letter, Linden and Holder interview her teacher Bennet Ahmed. He denies having anything to do with her death but provides them with new information, a super 8 film she made. They learn something interesting about Ahmed's wife, Amber. On the campaign trail, Richmond's ads are having the desired effect but he still trails the incumbent mayor. At Gwen's urging, he approaches Mitch Larsen but can't quite bring himself to use her. He's still trying to find the mole in his campaign. Stan and Mitch find that friends and customers alike are avoiding them. A frustrated Stan decides to get his on information on what may have been going on at Rosie's school.
Having found ammonium hydroxide in Bennet Ahmed's apartment as well as on Rosie's clothes and body, Linden is now certain that she was at his apartment on the Friday night she disappeared. Interviews with Ahmed's neighbors give them eye witnesses stating they saw Rosie enter his place. Darren Richmond has more problems when he learns that Ahmed, an active member of his main community project and someone who has even appeared on his campaign commercials, is the main suspect. A debate with the mayor on live TV does not go well. For the Larsens, it's the day of Rosie's funeral. Stan is told who the main suspect is and he takes Ahmed for a ride.
After Rosie's wake, Stan take Bennet Ahmed for a ride, intent on taking his revenge. Linden's relationship with her fiancé faces a crisis as she and her son Jack miss their flight. Linden re-interviews Amber Ahmed who reveals that she was not entirely truthful as to her whereabouts on the night Rosie disappeared. Along with Holder, Linden visits a local mosque to see if they can get a lead on Bennet's friend Mohammed. Someone slips them an address which leads them to an interesting encounter. On the campaign trail, Darren Richmond is pre-occupied with an upcoming parole hearing for the drunk driver who killed his wife. He refuses to ask Ahmet to resign from his main community project and pays a heavy price at a City council meeting.
Having possibly ruined a long-term terrorist investigation, Linden and Holder face the prospect of having their case shut down completely. The Feds aren't cooperating so Linden takes matters into her own hands, confirming that a key piece of evidence, Rosie's sweater, is at the scene. Shut out of the case as a result, it's left to Holder to suggest a solution on how they might go forward. Darren Richmond meanwhile attends the parole hearing for the drunk driver who killed his wife. He decides to release the information they've obtained on the Mayor's extra-curricular activities. Linden's personal life is in a shambles. Her fiancé is refusing to return her calls and her son Jack is lashing out at what he sees as his mother's lack of interest in him. Mitch and Stan Larsen's relationship begins to deteriorate after they begin to blame each other for happened to Rosie.
Now aware that her partner has forged the key piece of evidence that led to the arrest of mayoral candidate Darren Richmond, Det. Linden again delays her departure. Linden tells her boss and he gives her the okay to continue the investigation. She is beginning to see the possibility of a larger conspiracy. Richmond is seriously injured and in a coma. His staffers Jamie and Gwen are at the hospital waiting for news from the doctors and are desperately trying to get in touch with his next-of-kin, his sister. Holder seems lost and doesn't quite understand what is going on. The police have arrested the shooter, who is Stan's employee Belko. At home Stan is having problems not only with Rosie's death but also with the fact that Mitch has left. He's stunned when Linden tells him Richmond is innocent and the charges will be dropped. He asks Terry to stay with them. At the police station, Belko has a run-in with the police.
Stan is shocked when he finds that someone has left Rosie's backpack on his doorstep. He contacts Holder who takes possession of it and hesitantly agrees to provide some police protection. Oakes is quite specific about what he wants Holder to do with the backpack. Holder plans a little subterfuge of his own. Richmond awakens from his coma and learns that he is paralyzed from the waist down. Linden gets some key information from Gwen who also gives her a key to Richmond's apartment. There she finds information that begins to explain just what he was doing the night Rosie was killed. Holder is desperate to speak to Linden but she will have nothing to do with him. A frustrated Stan turns to Janek to get satisfaction.
Mitch is on the road but can't help seeing Rosie anywhere she looks. Linden continues to track Rosie's movements after she was last seen at the casino just after midnight. She's also trying to learn the identity of the man with the strange tattoo. She learns of Rosie's backpack from Stan and gets it from the now retired Lt. Oakes. She quickly realizes that Holder switched the backpacks. There's a fire at the shoe store where the Beausoleil escort service kept its computers. CCTV footage from the area around the store shows the man with the tattoo driving one of Stan's trucks. Darren Richmond is determined to continue his campaign. Gwen is thinking of leaving Seattle and taking a position in Washington. Stan is upset when Janek gives a gift to one of his boys as he doesn't want them to know about his past.
Linden and Holder continue their search for the man with the odd tattoo. They eventually identify him as Alexi Giffords, a young man with a long juvenile record who lived in foster care for 10 years. They also find that he lives 3 blocks from the Larsens. They're also keeping an eye on Stan Larsen and begin to wonder if he is back with the mob. Stan goes to pick-up Belko Royce's remains only to learn that Janek has already taken care of it. Holder tell Linden that he thought the incriminating photo of Richmond was legit and he just put his trust in the wrong people. Darren Richmond meanwhile begins his therapy and the Mayor pays him a visit, promising to support him in the next election. As if she doesn't have enough on her hands, Linden learns from her ex-husband's attorney that he will be seeking joint custody.
Holder and Linden learn that Alexi Giffords' father was killed by Stan Larsen when Stan was still doing muscle work for Janek. They arrest him but Lt. Carlson gives them only 8 hours to get a confession. Alexi denies any involvement in Rosie's death but the police realize Rosie was in trouble having found a voice mail message from her saying 'I saw him again'. Alexi says Rosie had also learned a family secret. Mitch has yet to contact anyone in the family and her parents are worried. They're also openly questioning whether Stan is fit to take care of the boys. Mitch gets to know the teenage girl from the motel and buys her lunch. Darren Richmond decides to drop out of the race for mayor, much to Jamie's consternation. At the end of a long day, Sarah gets back to the motel to find her ex-husband there waiting for her.
Stan tells Det. Linden he has no idea who Rosie's father is but knew before he married Mitch that the child was not his. She assures him that Alexi Giffords had nothing to do with Rosie's murder. Stan is keeping a watchful eye on him nevertheless. Terry has been seeing the married Michael Ames but he breaks up with her. Michael Ames becomes a suspect with Linden and Holder wondering if he might be Rosie's biological father. It turns out Rosie may have been blackmailing Ames by threatening to tell his wife about his affair with Terry. They re-question Michael Ames and learn who sent the blackmail threat. Darren Richmond meanwhile gives an interview and re-affirms his desire to run for mayor. Gwen has a change of heart and returns to Seattle hoping to rejoin the Richmond campaign. Mitch continues getting to know her new friend. Det. Linden and son Jack moves out of their hotel after it becomes apparent to her that someone had earlier broken into their room.
Linden and Holder return to the casino. While Holder tries to get information inside the casino, Linden explores the rest of the island. Linden learns that there are rooms where working girls can ply their trade. He also learns that there are new rooms under construction. The casino manager and the tribal police take a dim view of their investigation. Having been publicly branded a killer - and with the election only one week away - Gwen tells Darren Richmond that they need the Larsons to publicly exonerate him from anything to do with their daughter's death. Stan refuses but later has a change of heart. Stan learns about Terry's relationship with Jasper Ames and he throws her out of the house. Linden's personal problems continue when she's visited by two child protection officers who have received a complaint about Jack's welfare.
Linden has to fight Lt. Carlson to get the police out to search for Holder. He's not keen to go onto Indian tribal lands but Holder is found alive though severely injured. Linden pays a heavy price however. Linden keeps Holder's rendezvous with the young woman who found and returned Rosie's backpack. She tells Linden exactly what Rosie was doing at the casino that night. Richmond leaves the hospital with 5 days to go before the election. Gwen and Jamie tell him he's he's losing by 7 points and either has to tell the public where he was the night of Rosie's murder or make some type of grand gesture. After his television appeal, Stan Larsen receives a number of tips about his daughter's murder but Linden doesn't put any faith in the information he's received. Stan learns that Linden had good reason to be skeptical. Linden decides to send her son to live with his father.
Holder can't find any of the files related to Rosie's death and learns that the entire case has been transferred to the County. Holder follows up but is told by County that the files never arrived. He thinks he knows where they are however. With Rosie's key, Linden goes to the construction site at the casino. She's convinced Rosie saw something there that led to her death. Mitch Larsen visits her old boyfriend David, whom Rosie had visited with questions about her mother. Stan Larsen meanwhile has to deal with son Tommy who's gotten into trouble at school. Darren Richmond meets with Nicole Jackson about the possibility of an endorsement but isn't prepared to meet her terms, even if it costs him the election.
Linden wakes up in the hospital psychiatric ward after casino personnel told the hospital she tried to jump off the balcony and resisted their efforts to rescue her. Her dismissal of that claim and the fact that she is working on a high profile murder case fall on deaf ears as do Holder's attempts to convince them otherwise. He tries to enlist Reggie's help but in the end has to turn to someone else in Linden's life to get her released. Holder is still investigating the case and is simply ignoring his Lieutenant's orders to stay out of it. Holder learns from a patrolman that one of gangster Janek Kovarsky's men was caught trespassing on the waterfront construction site the night Rosie was killed. He was never charged after being vouched for by the construction manager. It all points to deeply rooted corruption in the Mayor's office.
Although she is now out of the psychiatric ward, Linden will not give up on the investigation. She asks Gwen to use her father's influence in Washington to get a federal warrant to search the casino. Gwen has a tense confrontation with her father but gets it in the end. The FBI raid the casino and apparently find nothing. Linden has in fact recovered the city hall key card she saw. It doesn't lead them to the Mayor's office as expected but to another office in the building. Stan meanwhile is ordered by mobster Janek Kovarski to eliminate Joseph Nowak. Stan refuses but Janek knows how to get what he wants. He's in for a bit of a surprise however. When Stan gets home, there is a surprise awaiting him. On the election trail, Richmond is facing the public disclosure of his attempted suicide.
Election day has arrived and the detectives have traced the City Hall key card to someone in councilor Richmond's office. Realizing they are about to be arrested, they make a deal with Mayor Adams: they will keep quiet about the doctored photo that led to Richmond's arrest if he will call off the police and let them finish their investigation. They soon have it down to two suspects, whom they've dubbed Donnie and Marie. Security camera recordings seem to give them the culprit. Meanwhile, Mitch is back home but having trouble re-adjusting to the environment. She learns about the house Stan bought just before their daughter's death. He sees the house the house as a new beginning; she sees moving from their current house as abandoning Rosie.
Detective Holder and his new partner investigate the murder of a 16 year-old hooker who was stabbed and had her throat slit. The medical examiner determines that she has defensive wounds and the knife used had a serrated edge. He and his new partner have had a good year solving all seven murders they've investigated. Holder has also given up some of his bad habits and will soon be writing his sergeants exams. Holder notices a similarity between this death and one that Sarah Linden investigated a few years before. In that case, Ray Seward was convicted of killing his wife Tricia Ann and is now on death row awaiting execution. Holder visits her to discuss the case but she's not keen to reopen a case she solved three years ago. She now works for the Seattle ferry system and has a new boyfriend. All in all, her life is good. As she reviews Holder's case file however, she is slowly drawn in.
Bullet reports that Kallie Leeds is now missing and no one seems to have seen her after she left the shelter the previous evening. With Ray Seward opting for execution by hanging, correctional officer Francis Becker begins to review the procedures. Linden is disturbed by some of the coincidences she's found in Ashley Kwan's case and expresses some doubt about Seward's conviction to her former partner James Skinner. He's satisfied they did the right thing but Skinner's wife tells Linden to stay away from them. She next visits Seward's son Adrian who had drawn her a picture which she now recognizes. When she locates the site, she finds something that's quite grim. On death row Seward cons one of the correctional officers, Evan Henderson. into letting him make a phone call, supposedly to his lawyer. Becker is none too pleased and ensures Seward knows exactly what he's in for.
Adrian's drawing leads Linden to a killing ground where the police find a total of 17 bodies. All are of young women - some could be as young as 13 - and Linden, who accepts reinstatement as a detective, is put in charge of identifying the bodies. The coroner can give her little to go on but says its possible the women were killed in the same way as Ashley Kwan. He can confirm that the women were all killed several years ago but over a short period of time. Since Kwan was held for several days before being killed, Holder begins looking for the missing Kallie Leeds. A distrustful bullet points him in the direction of Goldie and while they don't find Kallie they do find that he is involved in kiddie porn. At the prison, Ray Seward has gotten his hands on a razor blade.
Linden and Holder aren't having much luck identifying the voice of the man who spoke to Kallie Leeds on the dvd they seized. The police raid the motel used by many of the prostitutes and a special room behind a false panel. Linden matches one of the 17 bodies to a girl in the video. She also finds one of the women on the dvds but she says she doesn't remember the man who questioned her. Linden thinks she's hiding something. Similarly, Kallie's mother says she never heard the voice on the recording but Linden thinks she's lying. Goldie turns the tables on the police and goes to the press who dub the killer the Pied Piper.
Kallie's mother Danette tells her boyfriend Joe Mills that she's starting to worry about Kallie. He tells her she has nothing to worry about. The police continue their search for Joe. Mama Dips denies even knowing him but Linden sees through her and determines the relationship between the two. They also learn that she twice called Joe at Danette's trailer. By the time they search Danette's trailer he is nowhere to be found. They get a solid lead when a teenager reports nearly hitting a badly injured girl with his car. They trace her steps and find a bloodied biohazard bag - but no victim. As they continue to search the city, they find blood evidence suggesting she may have gone to the teen shelter. There's no sign of her there but Bullet shows them where she might be staying. When they do catch up the girl, they find it's not Kallie. Danette's mother makes a horrifying discovery.
Linden and Holder question the girl they found, Angie Gower. She was badly beaten and had several of her fingers severed. She says her attacker was soft-spoken and said he was going to save her. She doesn't recognize any of the suspects' photos, including Joe Mills. Holder is beginning to think they're looking for the wrong guy. A terrified Danette Lutz goes to the police station to speak to them about what she's found. Linden has little respect for her but Joe Mills has disappeared. Linden wants to get permission for Adrian to visit his father in prison but his foster parents won't hear of it. Information from them lead Linden and Holder to the apartment where Seward's wife was killed and Linden is now convinced Adrian saw the killer. Skinner isn't impressed however. At the prison, Seward faces someone from his past and gets an unexpected visitor.
Linden and Holder now suspect Pastor Mike as the man responsible for the murders. They have no proof however. Kallie's mother is still looking for her and visits the pastor who tells her not to lose hope. She finds a note on her windshield. Bullet and Lyric hook up. Bullet tells Holder that there's no way Pastor Mike is the killer. They get an eyewitness who saw the pastor with Angie Gower and learn Pastor Mike has a secret. At the prison, Seward razzes Becker for missing his shift during the death on cell block. Linden's boyfriend - or former boyfriend - wants to know what she's doing but she tells him it's over.
With his secrets unveiled, Pastor Mike takes Linden prisoner and they drive around the city. Linden manages to keep her radio on and the police are able to locate them. Linden believes him when he says he's not the serial killer and forensic analysis of his car seems to suggest he is innocent. Bullet is frantic over the missing Lyric, convinced that Pastor Mike has taken her. She tells Holder Mike has taken her to the woods where they found the killing field. The police diverted resources to look for her and it's apparent Bullet lied when they find Lyric out hustling on the street. For Bullet, Lyric's reaction to what she's done for her isn't quite what she was expecting. She talks to Angie Gower. At the prison, Seward pleads with his lawyer to do something, anything, based on Linden's belief that he is not guilty of killing his wife. The lawyer says nothing can be done.
Kallie's mother Danette Lutz is still looking for her and returns home to find Joe Mills waiting for her. He beats her and is long gone by the time the police arrive. The police do get a break in the case when they learn Mills had a storage locker. Holder and Linden check it out and find that Mills has been living there. They practically wrap up the case when they find trophies belonging to several of the dead girls. They're not prepared for what they find in the trunk of his taxicab. Ray Seward's execution is fast approaching. Linden finally gets permission to interview Seward's son Adrian and he identifies the killer. It doesn't add up however. Twitch and Lyric find a new place to live.
It's now 12 hours to Ray Seward's execution and Linden is still trying to get a stay of execution for him. Seward identifies his wife's ring from among the trophies found in Joe Mills' storage locker but it is insufficient to convince the Attorney General. Adrian is also at the prison having been promised the opportunity to see his father. He has information for Linden as well but Seward can't shed any light on who might have killed his wife.
With the execution of Ray Seward and Joe Mills about to be charged with the death of the young women, Linden and Holder try to put their lives back together. Linden renews her relationship with an old friend. Holder attends Bullet's funeral and then tries to make things right with his girlfriend Caroline. He also makes amends with his old partner, Carl Reddick. The detectives are called to the scene of a murder after firemen find a body inside a burnt out car. The coroner identifies the victim as a female who died sometime the previous day from a gunshot to the head. Whoever did it took out all of her teeth - and her ring finger is missing though it's a somewhat older injury. They think they have found Angie Gower. Holder thinks the only person who would have known about Joe Mills and who could have planted the rings to frame Mills would be another cop. Linden figures out how Adrian Seward was able to complete his drawings. At the prison, Becker tells Henderson that he's decided to retire.
Holder and Linden now believe that a police officer framed Joe Mills for the murders of the young women found in the swamp. When they learn that an officer known to both of them lived next door to the first victim, they think they have their man. With Angie Gower having been killed, they fear for the worse when Adrian Seward goes missing as it seems the killer is now tying up loose ends. As Linden tries to tie things up, Carl Reddick is nowhere to be found, Holder is pulled in by Internal Affairs for questioning and Lt. Skinner's marriage has broken up forcing him to move out of his house. Linden finds the proof she needs to definitively identify the killer when she spots Kallie Leeds' ring.