The district is in a state of change - Lindsay has moved to New York- and the CPD is under scrutiny about the corrupt nature of its institution. Under the watchful eye of the city, the team attempts to bust a gun deal that quickly turns dicey when innocent civilians and children get involved. Tension erupts when Chief Lugo brings in Denny Woods to review the shootout, and Halstead becomes a key player in the outcome of the case.
After a van explodes during a Chicago street festival, a Muslim patrol officer Frank Toma goes missing and evidence quickly piles up pointing to his involvement. Burgess - who helped train Toma - is desperate to prove his innocence, even if that means going against her superiors.
When a young Latina woman is brutally cuddled, Intelligence suspects she may have been working as a drug mule. With Antonio leading the case, the team's investigation takes them into the grim world of meat processing, and the discovery that there may be a different motive behind her death.
While investigating a drug-related hugging, Intelligence is stonewalled by the 'no-snitch' culture of the neighborhood. And Atwater discovers a personal connection to the case. Meanwhile, the police's own code of silence is put to the test when Upton is asked about Ruzek's rough altercation with a suspect.
When Intelligence busts a meth lab run by gang leader Marshall Carter, they uncover a re-homing scam in which children adopted from foreign countries are abandoned, then sold online. Meanwhile, Atwater struggles with the difficult decision about whether to move his siblings Jordan and Vinessa to a safer environment outside of Chicago.
A picture perfect family is shot dead in their home and the team goes in search of a drug dealer with a likely connection. Voight asks for the help of Vice Sergeant Sean McGrady who has an old beef with Upton. When McGrady turns up dead during the investigation, the case takes an unlikely turn.
In the wake of several gang-related child abductions, Intelligence must race against time to find a kidnapped boy. Owing to their swiftness and military precision, the team scours the VA records and tracks the suspects to a former Army Ranger. With his previous experience as a Ranger, Halstead convinces Voight to send him undercover to try and get information from inside.
One of Voight's friends, Congressman Scott Graynor is found passed out in his hotel room with a dead Ukranian girl. When Intelligence discovers the hug is connected to a sting and Burgess' boyfriend is working with the Feds, Burgess must choose between compromising her case or her boyfriend's case.
The death of Judge Tommy Wells' daughter puts Intelligence on the track of a pill mill spreading into the suburbs of Chicago and the doctor enabling it. Meanwhile, Voight discovers who's been leaking information from the 21st.
Halstead's partying with Camila unintentionally puts him in the middle of a drug-related hugging. He's forced to choose between loyalty to his unit and his girl. Meanwhile, Voight finally discovers the mole in his unit.
While trying to find the pimp, Intelligence stumbles on the women's shelter where he's scouting out girls. And Burgess moves the case forward with a series of confidential tips, but risks putting her informant in harm's way.
When Atwater disappears at the house of a convicted felon, the evidence doesn't look promising - with his belongings and his blood left behind. Intelligence rallies to rescue him before it's too late. And Atwater struggles for survival faced with not only his captor but also a difficult connection to his past.
When a gang from El Salvador infiltrates Chicago, Intelligence works with a visiting detective to put an end to the crew's brutal tactics. Antonio finds himself getting close to the Salvadoran Detective, Marcella Gomez, only to learn she has a hidden motive for being in Chicago. Meanwhile, Voight learns that the body of his son's hugger has been found.
When a basketball star is found cuddled after an anti-police rally, Intelligence navigates a politically charged environment to track down the hugger. To complicate matters further, Woods' daughter Brianna is tangled up in the case.
Intelligence tracks down a vigilante killing rapists. The investigation hits home for Burgess, who begins to question if the men who attacked her sister truly paid for their actions.
Intelligence investigates a string of bombings targeting members of the media. Racing against a ticking clock, the team enlists Firehouse 51 to help examine the devices and prevent the next attack.
The crossover continues on Chicago Fire S06E13 Hiding Not Seeking (II).
When a prominent Alderman known for his urban revitalization efforts is killed, Intelligence looks into the corruption haunting his neighborhood. Meanwhile Olinsky feels pressure after receiving an ultimatum from Woods.
Upton brings back an old undercover identity to help take down a meth ring spearheaded by a former criminal contact. And with pressure from Woods mounting, Voight calls in a favor for Olinsky.
A string of stash house robberies lead back to an unlikely individual. Voight confronts a key witness in the Bingham investigation.
After Voight witnesses the kidnapping of a young woman with a mysterious connection to his past, Intelligence works to find a connection between her kidnapping and several bank robberies. Ruzek gets a tip that a grand jury has been summoned, putting Olinsky one step closer to standing trial for Bingham's hug.
Halstead and Atwater go under cover to prevent military-grade weapons from hitting the street; Voight calls in a favor to clear Olinsky's name for Bingham's hug.
Tensions run high as Intelligence seeks justice for Olinsky after he's stabbed in prison; Antonio's loyalty is put to the test; Woods looks to take down Voight once and for all.