It's the night of the 15th of March, 2009, and a tramp called Landry enters the local convenience store for another drink. The owner, Henry "Pops" Walters, smells the booze on his breath so he convinces Landry to take a cup of coffee instead and sends him off. Soon after, he hears the door opening again. He turns around thinking it's Landry, instead finds a gun pointed at his face.
At about the same time, detectives Will Jeffries and Nick Vera are working the night shift, patrolling the streets and bickering over the choice of radio programmes. Jeffries then pulls over saying he needs to buy milk and enters Pops' store, leaving Vera snoozing in the car. He walks straight up to the fridge but feels there's somebody at his back. He tries to reach for his gun... The next moment, Vera is awoken by two gun shots. He dashes to the store with his gun held up high and finds the owner lying face down, in a pool of blood. Jeffries, curved on a side, is barely breathing, blood all over his clothes. Vera immediately dials 911 for help, shouting repeatedly "Officer down! Officer down!".
Jeffries and Pops are rushed to the hospital OR while Vera looks shocked and confused. All the other team mates are informed of the situation and they immediately head for the crime scene. Lt. Stillman reaches Vera at the hospital where they wait hopefully for some good news from the doctors.
In a few minutes, the crime scene is filled with policemen and police cars. An officer informs Lilly that Pops, the store owner, has deceased, while Jeffries' condition is still unknown. A detective, Pete McGinley, explains to detective Miller what could possibly be the reason behind the shootings. Scotty yells at the crowd of spectators for any witness to come forward. He spots Landry, who claims he's heard three gun shots when he was crossing the street. Scotty takes him in custody as a potential witness. Lilly and Scotty then enter the store and study the scene. Scotty finds two very old surveillance tapes. Lilly recognizes a young lady from a photo hanging on the store's notice board. She had seen her at the police station a couple of weeks earlier, anxiously talking to Jeffries about a certain "Valentine" who was in bad terms with her grandpa, Pops.
At the hospital, Vera tells Lt. Stillman what happened in the few minutes after he called for help – he heard someone going out the back door and soon after another cop (McGinley) broke into the store and went after the suspect. He found it rather strange that a cop could reach the crime scene so quickly. Scotty reaches the hospital where Vera and Stillman are waiting for the doctors to come out. He fills them in on their findings at the store. Vera recalls taking down a phone message, two months earlier, from a police officer about a certain "Valentine" being accused of gun possession. Stillman searches Jeffries' wallet for Valentine's phone number but finds Jeffries was carrying an unusually large amount of cash with him. When Stillman hears McGinley is involved with the case, his facial expression changes and he leaves for the police headquarters.
At the police headquarters, DA Curtis Bell tells Lilly that James Valentine has juvenile records; he joined the military in order to avoid hard prison and has been clean ever since. Kendrick, the detective who had left a message with Vera, later said he had made a mistake about Valentine. Lilly tells an officer to track him down – apparently Jeffries had asked Kendrick for a personal favor by closing an eye on Valentine.
Scotty learns from agent Frankie Rafferty that one of the surveillance tapes was unusable but she promises to try and find something on the second tape. Stillman takes McGinley aside and confronts him on why he was tailing Jeffries. McGinley had picked pictures of Jeffries getting money from Valentine so he concluded Jeffries was probably dealing with drugs. Meanwhile, detective Miller talks to Carmen, Pops' granddaughter. She's visibly shaken by her grandfather's tragic death but manages to tell the cops in which restaurant Valentine works.
Lilly and Scotty make sure Valentine's alibi is confirmed by the restaurant camera. Then they interrogate him. Valentine says he was grateful to Pops and would have never harmed him. He was trying to buy a gun to protect Pops from Francisco Ariza, a local thug who was threatening Pops into accepting his protection. Jeffries, however, stopped him and was probably going to return the money to Pops on the night he was shot.
At the hospital, Vera can't sit still so Stillman takes him to the hospital chapel and tells him to pray. Miller reaches them there and shows them Ariza's folder. As they talk, another man, who is also praying, complains he's getting disturbed, causing Vera to lose his temper. Stillman tells him to chill out - after all, they are in a chapel. Then the doors open and the surgeon comes in and tells them Jeffries is going to be fine. They all breathe a sigh of relief.
Rush and Valens break into Ariza's apartment. Nobody is in but in the trash can they find blood-stained clothes and shoes. This is enough to call for a search warrant. When they get back to the police headquarters, Lilly finds her dad waiting for her. She's surprised to see him but hides it very well. He heard on the radio that a homicide cop was wounded in a gun shooting and was worried about Lilly. Before leaving, he gives her a medallion that may keep her safe. She reluctantly accepts it but is annoyed at his belated concern for her safety since he didn't even show up when she actually was wounded.
Lilly then heads to the hospital while Valens and Miller go to Ariza's aunt's apartment where his GPS was last located. The cops turn things upside down at Beatrice Calderon's apartment, while Miller and Valens try to persuade Francisco's aunt and younger brother Gabriel to talk. Gabriel seems very upset but says the old man deserved it. He recalls that one day, he and his brother entered Pops' store and were treating themselves to chips and popcorn when the old man had commanded them out because Francisco didn't want to pay for the snacks. Pops humiliated his elder brother by telling him to sweep his store for a minimum wage instead of running after easy money and dodging bullets. Annoyed by their arrogance, the detectives take them both to the station for further questioning.
At the hospital, Stillman looks from a distance at a convalescent Jeffries, through a glass panel when Department Commissioner Patrick Doherty comes up to him. Evidently, McGinley has reported Stillman to Doherty because the two start arguing on interfering into each others' responsibilities in the case. Stillman says he can prove Jeffries was retrieving stolen property and threatens Doherty to leave his team in peace.
Jeffries wakes up and finds Lilly sitting at his bed side. He asks about his friend Pops but Lilly shakes her head . Jeffries remembers how Pops changed his life, pulled him out of the whirlpool he was sinking in after his father left his family. Lilly tells Jeffries they're looking for Francisco everywhere but still can't find him. Jeffries hints to his other girlfriend's home.
A team of cops breaks into the girlfriend's flat, Rush and Valens following close behind. However, they're too late, Valentine got there first and shot Ariza in the chest. The officers arrest Valentine and take him to the police station. Looking at Ariza's dead body, Rush notices the size of the clothes and shoes they found earlier doesn't match Francisco's - this means Valentine killed the wrong man. They interrogate Valentine and tell him he made a dreadful mistake but he rebuffs the accusations saying Francisco himself told him he did kill Pops. Francisco was obviously trying to protect somebody.
In the hospital chapel, Nick sees the man he had previously assaulted, apologizes to him and even hugs him. They're interrupted by Miller who's come in to check on her colleague. Vera is not in the mood of getting some sleep but it starting to rely much more on prayers, yet neither of them can make sense of what has happened to Will.
Agent Rafferty enters Stillman's office with the surveillance tape she's been working on. She shows Rush, Valens and Stillman the recording – in it, Francisco Ariza is seen shaking hands with Pops, few hours before the shooting took place. This confirms the fact that Francisco couldn't have killed the store owner. Valens notices something on Ariza's coat and figures out who it was that Francisco was trying to protect in his last moments of life. He goes to get Gabriel but the officer in charge of him had already let him go, thinking he was harmless.
Again Valens and Rush break into Ariza's apartment with their guns held up high. They call out for Gabriel and he comes out and shoots at them. They manage to duck behind a wall. Rush fires back, wounding the boy's leg. He drags himself inside the bathroom. Valens nods to Rush to get Gabriel from behind and starts talking to him and telling him his elder brother wouldn't be proud of what he's done. Gabriel starts crying and recalls the look on his brother's face when he saw him coming home covered in blood. Rush gets him in the line of fire and orders him to surrender. Gabriel sees he's out of options and finally drops his gun. The cops arrest him, and take him away on a stretcher.
In the final scenes, as The Judgment by Solomon Burke plays along, Valentine lies in a prison cell thinking of how he threw his life away, Stillman closes the murder cases of Ariza and Pops, people lay down flowers, candles and cards outside Pops' store while his granddaughter watches on and from his hospital bed Will sees Pops nodding at him, then he looks at Vera finally sleeping on the couch next to his bed. Lilly locks herself in a double mirrored room, she looks at the medallion her father gave her, starts crying and falls down to her feet.