After being dismissed from the hospital, Lilly returns to the police department and her teammates welcome her back. She is determined to throw herself 24/7 into her job in order to overcome the shock caused her by the recent shooting, which took place at the police department and nearly cost her life. Special security measures have been taken at the department to avoid any sort of replica of the disaster but the still-broken windows keep reminding everybody of the latest facts.
Urged by a frustrated and disillusioned mother, accusing the police of killing her son by arresting him for a murder he didn't commit, Lilly takes the lead in the re-investigation of a 1994 closed case.
In September 1994, the bodies of three kids – Jack Raymes, George Russo, and Sean Costley, all aged 10 – were found in an abandoned swimming pool, together with their bikes. They had been beaten up to death and their eyes had been taped shut. Det. Joe Connolly conducted the first investigation, which led to the arrest of two teens, Dylan Noakes and Teddy Nimmo. The latter had committed suicide in his prison cell just after his 30th birthday, causing his mother's anger to storm into the police department. In his cell was also discovered a note referring to the murders. At first, the detectives think that Nimmo himself had written it, but his mother reveals her son was illiterate. Further, the probe reveals the note was sent from outside the prison.
The team starts the inquiries from now-retired Det. Connolly, moving on to Jack's parents and reaching out to Dylan Noakes, in prison. Lilly attentively analyses the photos of the crime scene and notices that the bikes were far too clean after the heavy rain of the previous night, thus concluding that the kids were murdered elsewhere and the bodies and the kids' bikes moved to the site later. The detectives also discover that Connolly had, by means of violence, extorted a fake confession from Teddy Nimmo, finding him the weakest of the two friends.
Finally Lilly must talk twice to Dylan Noakes, before being convinced that he's innocent. He says he had found Jack in a crawling position with his teddy bear tightly clasped within his hands. This suggests Lilly that Jack was murdered in some familiar place. They then turn to Jack's short-tempered father.
All the way long, Lilly seems to be a step ahead of the others but Lt. Stillman minimizes her efforts by assigning the case to Scotty and ordering Lilly to go to counseling. When it comes to entering the double mirrored room to question Jack's father, Lilly keeps having flashbacks of the shootings and therefore must step back. She goes to the restroom to cool down and meets with Jack's mother. Mrs. Raymes accuses the police of unjustly suspecting an innocent and kind man such as Jack's father but Lilly wastes no time in self defense and reveals her some details of the investigation. She asks her to come forward with any information or evidence her mind has removed due to painful memories. Jack's mother is carried away by her words and remembers finding her husband's flashlight broken and blood stained. He used to carry the torch everywhere because he has always been deadly scared of darkness because of some even that happened to him in his childhood. This explained why the kids had their eyes taped: he had killed them with the torch in a moment of rage and, as a further punishment, he had taped their eyes so they would always stay in the dark. Thanks to this information and the change of attitude of Jack's mother, the cops are able to make him confess his crime and thus arrest the real culprit.
In the end, Dylan Noakes is freed and Teddy Nimmo and the three kids can now rest in peace.