In the season premiere, 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. At District, Burgess meets her new partner, Sean Roman and tension is high from the start. Soon she 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 - her mom, Bunny.
Intelligence begins to look into a string of murders where the victims have a dollar bill pinned to their chests. Thanks to some digging by Ruzek , Voight learns his friend was involved in some shady business dealings. Antonio and Halstead follow-up on some leads that help focus in on the culprit and motives for the murders. Meanwhile, Burgess and Roman investigate a series of house break-ins and get some help from Desk Sgt. Platt.
The bounty on Halstead's head becomes a serious reality as an innocent bartender takes a bullet meant for him. Olinsky tries to reason with Bembenek to call off the hit, to no avail. Voigh and the team keep this investigation in-house to find the hired assassin. Meanwhile, after a tense interaction at district Platt and Nadia come to an understanding.
Two teenage girls have gone missing and the team know the clock is ticking to find them. Halstead, Antonio and Lindsay investigate a tenement which gives them a much needed lead. Voight brings the father of one of the girls to district in order to get some honest answers. Meanwhile, Platt puts Roman and Burgess on gun buy-back duty where they ask questions when they aren't supposed to.
While trying to help out Olive Voight is attacked and taken. When he doesn't show for work the team gets suspicious and begin investigating. Ruzek and Atwater prove they do belong on the team when they demonstrate smarts and savvy tracking down a lead that will hopefully bring them to Voight. Meanwhile Burgess and Roman are trying to track down a girl who has run off with a police badge.
Following the death of a 10-year old girl the intelligence unit have one option to gain access to their suspect, go on the inside. Ruzek and Atwater act as inmates to work the case from the inside. Outside prison, Voight and Olinsky follow-up on a good lead to answer some questions about the shooting. Meanwhile, Burgess and Roman show three boys around district thinking they are part of the Police Explorers program, only to realize that's not quite the case.
The final part of the crossover event finds our intelligence unit joined by detectives from New York's special victims unit to help solve the pedophile ring case. Ruzek and Det. Amaro along with Halstead and Antonio continue to hunt for the link to foster care and child trafficking. Meanwhile Burgess and Roman try to find the shooter from the hospital after using surveillance footage to identify him. Platt shows her deep respect for police and the dangerous work they do by honoring their fallen brother.
While Antonio continues his off-duty security job for Asher and Layla, Asher is killed. Voight and Olinsky make sure Antonio is covered. While they work the case Halstead and Lindsay go undercover in a rather uncomfortable location. Kot shows up to ask Lindsay for an answer.
Friend of Nadia's leads the intelligence unit to a huge heroin bust. Unfortunately this bust results in Olinsky arriving home to find the suspects are holding his wife. Voight and the team think they've found a common thread with the suspects but it's not who they think. Meanwhile Burgess and Roman are given an assignment where they get paired with a K-9 officer, Jenn Cassidy who is Roman's former partner and girlfriend.
With Burgess in the hospital after suffering gunshot wounds, the intelligence team is determined to find the people responsible. Lindsay delays her start so she can help with this case. Search of the house provides a lead and when a bomb is triggered a key suspect is found. Meanwhile the team takes turns watching over Burgess. Voight informs Burgess of a new opportunity that this affords her.
Lindsay has her first case with the task force and realizes she needs to call on Voight and the Intelligence unit to assist. Meanwhile Burgess is back on the job, but relegated to desk duty which allows Desk Sgt. Platt the opportunity to partner up with Roman.
Bob Ruzek is the first to arrive on the scene of a double murder. Intelligence arrives to take over the investigation tensions arise as Bob needs to hand over the case to his son and Voight. Lindsay's new gig has her planning a trip to Bolivia for an undercover investigation that could be for an extended amount of time. Burgess and Roman realize they need to put past events behind them so it doesn't jeopardize them going forward.
Antonio and his sister Gabriela go to the office of Elliot Gish, the man they believe started the fire that killed Shay. Intelligence along with patrol officers Burgess and Roman put pressure on Gish to try and make him confess. Lindsay approaches Voight about returning to Intelligence when she realizes that the task force isn't what she thought it would be. At the same time Desk Sgt. Platt is acting strange and has everyone curious as to why she's being overly cheery, friendly and nice.
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. Detective Gina Gawronski downloads their intel to the team, she also happens to be Antonio's former co-worker from Vice. Voight doesn't trust Bunny's motives for the tip.
With her recent decision to stay on the beat, Burgess begins to feel a little regret. While at a convenience store she sees some suspicious activity and pursues it without calling in for backup. Roman warns against it, but it's too late, Chang confiscates their guns and radios. They are trapped with no means to communicate out for support. Meanwhile, it's a slow day in intelligence and they are spending the day receiving taser certification.
Commander Fischer updates Voight on a missing officer that Narcotics had deep undercover with a robbery crew. Antonio connected with one of the crew members years ago, so he's asked to reestablish contact to help them find the officer. Meanwhile, Roman and Burgess are dealing with a squatter situation and they enlist Chicago Fire's Mouch to help.
With a World Trade conference in Chicago, all members of intelligence are undercover in various protest groups to determine potential threats. Ruzek, infiltrates the Black Grid group and befriends Sierra. When she ends up dead intelligence is suspicious of an Argentine Secretary, Fabian Sosa. Voight and Olinsky question Sosa about the death and the team enlists Mouse to help with their tech needs in tracking Sosa. Meanwhile Halstead's brother, Dr. Will Halstead shows up in town for an undetermined amount of time and is already stirring up trouble.
Intelligence responds to a drug robbery gone wrong and in their investigation it's revealed that the first person Voight ever gave his card to is linked to a double murder. Voight will fight to keep her family safe. At the same time, we learn the real reason why Halstead's brother Will came to Chicago. Meanwhile Desk Sgt. Platt takes care of a young girl at district.
When the father of one of the dead girls explains that he paid Dennis Lee to have her brought to America, this hits home with Olinsky. Lee is one of the Chicago's most wanted fugitives and escaped Olinsky once before. Intelligence isn't about to let Lee dupe them again and Olinsky's past files prove valuable in finding Lee's whereabouts. Meanwhile, Sean Roman has an altercation with a fellow officer which lands him in a bit of trouble. At the same time Platt helps prepare Nadia to take her polygraph test after passing the CPD written exam.
Continuation of Chicago Fire, "We Called Her Jelly Bean" episode. Benson has traveled into Chicago to help Voight and intelligence with a rape/murder case that is frighteningly similar to a case from New York a decade ago. She calls in Fin and Amaro to assist. The prime suspect, Yates is let go after rigorous questioning. He then requests a meeting with Lindsay and he warns of unintended consequences from what intelligence is doing.
As District 21 is struggling to come to terms with the loss of one of the team they are forced to put their personal feelings aside when a café is bombed. The unit has several suspects and only one good eye-witness, who happens to be a minor. Halstead pulls some strings to convince the mom to let him question Isabella on what she saw. Atwater finds himself in hot water when he makes a crucial mistake. Thanks to the tech savvy Mouse the team is able to gain important intel that could help solve the case. Meanwhile Voight helps Platt when she comes up against several roadblocks in an attempt to get a memorial stone for their fallen member.
When multiple people are shot inside an athletic club intelligence work to find and take down the shooters before there's any more victims. When they discover that all the targets were from the same law firm it's apparent that it is a case of corporate revenge. Now they need to find out what the motive for these killings. Atwater is dealing with his new assignment, while doing so he plays a key role in locating the shooters. Meanwhile Platt and Halstead are trying to approach Lindsay to see how she's coping with a recent death.
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.