The date is March 9, 2005. A man is sitting in a room watching TV while surrounded by teens. It's an old B&W film, The Maltese Falcon from 1941. There are charts on the walls saying things such as "Clean and sober". One of the teens complains about the choice of film; the man, the kids' counselor, calls him Corey. Another one is called Crystal. The man suddenly says it's time for them all to go to bed and congratulates them on "one more day clean and sober".
After they've all left, he comes back and turns the TV off, but hears some noises nearby. It turns out that Corey is holding another resident, Orlando, down on the floor while stabbing him repeatedly through the chest. Corey runs off and the man tries to save the victim. Two months later, the man himself is killed.
Now it's 2006. At the police station, Lt. Stillman tells detectives Lilly Rush and Scott Valens that someone has just tried to use a credit card belonging to the murder victim, Joseph Shaw, who was killed a year before, two weeks before he was due to testify in a murder trial against Corey.
Kat Miller asks Lilly if it's true she keeps pictures of murder victims on her bedside table while working on their cases. She admits she does, which Kat thinks is weird. It turns out this witness was shot in the face through a door window.
Lilly and Kat interview a couple called the Robinsons about their work at Robinson House, the rehabilitation center for teens with substance abuse problems. They also question the couple about Joseph, the man who worked there, as well as Corey, the supposed murderer. Jane Robinson says they set up the Robinson House after their son Tom died of a meth overdose. Jane tells Lilly and Kat that Joseph Shaw knew how to break through the barriers Corey was putting up. In a flashback, Corey goes cold turkey. Joseph, Jane and the other inmates comfort him.
In the present, Valens and Jeffries interview Corey at work, but he's not giving anything away. He says he doesn't have to talk about the case because the charges were dropped, but then he does anyway. In a flashback of a counseling session with Crys, Joseph, Orlando, and Corey, Crystal storms out, because she's obsessed with Joseph, but he doesn't want her and thinks it would be unethical. Valens and Jeffries finish interviewing Corey.
Lilly's at home with her ginger cat, looking at a picture of Joseph.
Jeffries and Miller interview Crys Eckersdorf, who's been living on the street again after Joseph's death. She tells them about Joseph's foster brother, Wilder Dautry, who interrupted a counseling session between them. She says that she didn't kill Joseph. She then tells them about when Wilder interrupted a counseling between her and Joseph. He asked Joseph for a deposit on a new place, but Joseph said he'd already given him all the money he had. He then threw him out, but Wilder stole his wallet.
Wilder turns out to have a long criminal record but nothing since May 2005.
In a flashback, Joseph asks his stepmother, Reba Dautry, to help Wilder come off drugs. He asks if they can go to the Dautry family farm, in an area called Limekiln Pike, although it wasn't maintained and all that was left was a shack falling down in an untended field. She gives Joseph the keys.
Lilly wants to go to the Dautry's farm late at night, but her boss Stillman tells her to go next morning. She goes alone later that night, anyway.
Lilly enters the shack, sees a startled cat, some framed photos, and a book about Robinson House. She is then shocked to see Joseph enter. "You're alive!" she says. She shows her police badge. She asks Joseph who got murdered in his apartment. He says his foster brother Wilder, so he let "them" think it was him instead. Joseph says he doesn't think the police can solve the case because "These people have the reach to stop you!" In a flashback, Jane Robinson tells Joseph not to testify against Corey. Lilly says she'll have to bring him in, but Joseph asks her not to, because he's not going anywhere. Joseph asks Lilly not to tell anyone he's alive. Lilly asks if it was him who tried to use his credit card. He says it was, when without thinking he tried to use it to pay for a vet after his cat, Laura, was bitten by a raccoon.
The next morning, Lilly phones work. She says she's at the Dautry Farm, but there's nothing there. Then she says she'll take a day off sick – something she's never done before! The other detectives are all very suspicious of this.
But instead of taking the day off, Lilly questions Ted Robinson about his wife Jane. She asks him if he knew that Jane told Joseph not to testify against Corey. Ted denies knowing anything about this, but says that if it actually happened, it must have been just to protect Robinson House. Lilly asks him how this would be protecting anything. Ted then says, "I think you're getting in over your head, detective!"
Crystal is still smoking dope, although she was at the rehab centre in Robinson House. Lilly goes to interview her on the street, while she begs for money to buy new strings for an acoustic guitar. She tells her that she saw Jane kissing Corey on the lips. She also told the murder victim, Orlando, about their affair, and Orlando had said that he was going to give Corey hell as well as blackmailing him. Corey decided to silence him by murdering him. Jane went to visit Corey in prison, and he told her what he'd done, but said that he'd only done it for her sake.
Lilly is talking on the phone with Joseph. She says he was right: she's found out what was going on and says she needs him to come to the police station. He says that if Corey doesn't confess, he'll be in danger. But Lilly assures him she'll make him crack, so he agrees to come in. Then there's a knock at her door: it's Valens. He asks Lilly why he couldn't phone her. She says she'd turned off her phone. He says she doesn't look sick at all and gives her a CCTV video of the person who used Joseph's credit card. He says he thinks she already knows who she'll see on the tape. Lilly tells him about her visit to the Dautry Farm and that she thinks she has feelings for Joseph.
Corey is now being held in a cell. Valens asks where Joseph is. Lilly says, "He's coming", then phones Joseph, but he doesn't answer. Lt. Stillman calls her into his office where he gives her a severe telling-off. He says she went off on her own while saying she was sick, lied to Valens, met a witness alone, went AWOL all day, then allowed the witness to remain at large when he needed to be brought in, but now he's disappeared and it's all her fault. At the end of this session, he tells her he doesn't know if the situation can be fixed.
Lilly and Valens try to make Corey confess while he's locked in a cell. They tell him Joseph's alive, but he doesn't believe them. Suddenly Joseph turns up to confront him. Corey tells them Joseph is supposed to be dead because "she" told him. When asked who told him, Corey says that Jane promised him after she visited him in prison and he told her what he'd done to avoid a scandal about their affair.
Lilly sort of admits to Joseph that she has feelings for him and Joseph tells her it's mutual. She asks him where he plans to go and he says back to the farm for the time being. He asks her if he should leave the door open in case she wants to track him down. She ponders it for a while but then tells him to keep it locked. Joseph is disappointed but then she continues: "I can break in if I need to."
Jane Robinson is brought in for questioning. Her attorney points out her good character over the years and rejects the accusations of a deluded youth. Det. Nick Vera presents them with the love letters she sent to Corey, including one dated only a week ago. Ted is shocked by this. It seems that Corey was a kind of substitute for their dead son Tom. He says she's been depressed since their son's death, which is something no parents should have to go through. He says they'd nearly recovered, when the murder happened and Joseph was about to destroy everything. He says, "She's all I have left. I'd do anything for her." Jane says, "Daddy", but it's not clear why. Ted then confesses that he decided to kill Joseph to stop him testifying against Corey. Unfortunately for him, although he went to Joseph's place to shoot him, he wasn't paying enough attention and it was actually Wilder who he shot. After finding the body, Joseph went away to the Dautry's farm.
We see Corey writing out a confession.
Just before the end, Lilly does the usual filing work to close the case, but this time it involves emptying the box labeled "J. Shaw" and putting all the evidence from that box into a new box with the same case number, but labeled "W. Dautry" and marked "Case Closed". She then removes the box labeled J Shaw.
At the very end of this episode, Lilly goes back to the Dautry farm, comes to the door and it seems she might be trying to break in, like she said earlier on that she might do. Then Joseph lets her in, so it seems they've started a relationship.