More is learned about Halstead’s dislike of the Rodiger family and it’s family relationships all around as Olinsky shows a paternal side with his daughter Lexi in an attempt to protect her and as Voight’s trying to help his son who has recently been released from jail. Meanwhile the Intelligence Unit investigates a counterfeiting operation after discovering some high end cloth-like paper. Sergeant Platt sends Atwater and Burgess to arrest a hoarder where they discover more than just clutter.

Voight's son may be involved with the Fitori murder case, intensifying tension between Antonio and Voight; Ruzek helps Burgess get retribution.

The Intelligence Unit works to find the bombers. Even with government agencies in the mix, Voight and his team work the case from their own angles and connections. Lindsay and Antonio question doctors who handled the transplant surgery for an Ambassador from Syria, but no clues emerge. Olinsky gets some solid intel and the team work from there. It’s a race against time as they realize there may be additional bombs targeted to detonate. Meanwhile Burgess sits vigil for her niece whose life hangs in the balance.

The crossover starts on Chicago Fire S02E20 A Dark Day (I).

Atwater is settling into his new gig on intelligence as Antonio is relegated to desk duty while recovering. Lindsay finally realizes she has no way out and confides in Voight for help. Meanwhile Jin is confronted about his secret meetings with Stillwell.

As the Sheldon Jin murder investigation moves forward, Voight is under close watch by Internal Affairs but he’s still in complete command of the intelligence unit. A routine undercover job becomes anything but when Voight’s SUV is T-boned while trailing an armored car carrying Ruzek. Burgess meets her new partner, Sean Roman and tension is high from the start, and she soon realizes there’s more to his story. After a long day, Lindsay pays a visit to someone she hasn’t seen in a very long time.

While trying to help out, Olive Voight is attacked and taken. Ruzek and Atwater prove they belong on the team when they demonstrate smarts and savvy tracking down a lead that will hopefully bring them to Voight. Burgess and Roman try to track down a girl who runs off with a police badge.

Bunny comes to Lindsay concerned about a suspicious repeat customer at her husband’s rental company. This lead brings Intelligence into a case which robbery-homicide has been working for months.

The investigation into the bombing of a trendy café hinges on a minor who witnessed it. A major blunder lands Atwater in hot water. Voight helps Platt in her attempt to get a memorial stone for the team's fallen member.

Retired Commander Perry enlists Voight and the team to help extract his cop nephew from a unit of corrupt officers who are robbing drug dealers. When things go bad Voight must take down a younger, more violent version of himself. Meanwhile, Lindsay struggles to stay clean. At the same time a woman from Olinsky's past reaches out to him.

A child abduction case hits too close to home for Dawson. Lindsay and Bunny's relationship reaches a critical impasse and Roman reveals his secret to Burgess.

Ruzek's job is on the line after an ill-fated undercover op.

Intelligence hunts down a crew responsible for a rape and robbery rampage. Lindsay is abducted on an undercover operation.

When Burgess and Lindsay respond to a call about a stabbing, the assailant turns out to be a kidnapping victim escaping her captor; Ruzek accuses Roman of having feelings for Burgess.

In the Season 3 finale, the team investigates the murder of a single mom who was in contact with Voight's now-reformed son, who was himself brutally assaulted. Meanwhile, Roman makes a major decision and Crowley plans to make changes within the unit.

The team investigates a murder in which the victim appears to have been wearing a CPD-issued wire. Burgess works a case with a new partner. Crowley questions Lindsay about the night that Intelligence pursued Justin's killer.

After receiving a complaint from a frustrated neighbor, Burgess and Officer Sorensen arrive to the house of baseball player Jake McCoy, and find the dead body of a 16-year-old girl, Maya Collins. There is conflict within the case as Intelligence learns that Olinsky and McCoy are friends, and McCoy admits that he was helping Maya and other girls try to escape the sex trade. Meanwhile, Burgess and Sorensen track down a thief who turns out to be a cop with a rocky past, and Lindsay gets a mysterious flower delivery that may be tied to her past.

When a mutilated sex offender is found dead, it is unclear if he was the victim of a hate crime, sexual assault or self-mutilation. As Intelligence questions those related to the case, they find themselves up against a private "special police" force who may be covering up illegal activities.

When a charred body is found in a torched house, Intelligence must work to identify the victim, as well as a young boy who is found badly injured inside. As they look to determine the cause and who may have been involved, they are faced with a web of secrets and lies. Meanwhile, Lindsay and Halstead receive an odd warning about Rixton that leaves them suspicious.

When Lindsay receives a panicked call from her mother Bunny whose boyfriend had just been shot, Lindsay must figure out the best way to approach the situation, as her mother is now a murder suspect. The case opens up when a group of high school students OD, and the drugs in question relate back to the situation with Bunny. In addition to her mother's issues, Lindsay finds herself up against the review board dealing with consequences of her actions.

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 murder 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.

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.