Pilot An unorthodox but effective FBI veteran, Charles Barker takes on rookie partner, Ellis Dove to train in his hard-edged and psychologically clever style of agenting. The mischievous Barker hazes Dove as they go undercover on their first case to infiltrate a weapons smuggling ring. Barker brilliantly manipulates situations, constantly tests his new partner's abilities and pushes him to delve deeper into the roles of the undercover characters he creates. Although Dove takes a liking to Barker, the new job takes its toll on him. The stress and danger of being an agent quickly makes him realize that he can no longer maintain normal relationships outside of work. Yet that's not the worst of it. The rookie is confronted with a larger challenge: An FBI Internal Affairs team feels Barker may have gone rogue and they try to enlist Dove as a double-agent in the bureau's investigation of his mentor.
Two Choices Barker and Ellis are assigned to take down a major drug trafficking ring run by a man named Jimmy Casserly - who happens to be in the Chicago Police Department's (CPD) custody. Barker fears that if Casserly stays in CPD custody, his drug deal won't go through and they won't have enough evidence to lock him up for good. The partners come up with a risky scheme to bust Casserly out of CPD custody and all is going well until a major wrench is thrown in the gears - an ex cop with a personal vendetta is also chasing Casserly. Meanwhile, Ellis continues to burn the candle at both ends. He runs into Rose and she questions what he does for a living, and Ray from Internal Affairs tries to convince him that Barker is crooked by giving him a DVD with supposed evidence against his mentor.
Nadia Barker and Ellis take on one of the nastiest and sleaziest rackets in the world - human trafficking. Barker goes undercover to take down a Romanian trafficking gang, while Ellis befriends Nadia, a prostitute who's been victimized by the thugs. Nadia's son was sold on the black market and ended up living with an adoptive family in America, and now Ellis is determined to help her get her boy back.
Infected Barker's old pal, Marcus, a security guard at ritzy jewelry store, gets Barker and Ellis involved in a nerve-wracking case involving millions of dollars and a deadly virus. Susan, the store's vice president, has stolen precious jewels in a desperate attempt to pay off the people who've allegedly infected her son with the virus. Barker and Ellis race the clock as they try to track down the blackmailers and figure out what may be threatening the boy's life.
Bitsy Big-Boy May Nan Nhung, a top nuclear physicist, has been doing some dangerous research, and now somebody's trying to kill her. Barker and Ellis face the tough job of keeping her alive and getting her to a meeting of the Nuclear Regulatory Commission where she's set to testify. But May Nan only longs to see her husband one more time because she knows she remains a target. Meanwhile, an injured Ellis is surprised when Rose drops by his apartment as he's getting out of the shower.
Hothead There's nothing more dangerous than an FBI agent who's gone rogue, and Frank Oland may be one of them. Barker, who trained with Oland at Quantico, sends Ellis undercover at the security company where Oland works to keep an eye on him. Ellis poses as an unpredictable and sometimes violent U.S. Marine to get close to Oland. The case gets even more complex when Barker searches for Oland's former girlfriend--who just happens to be one of Barker's former girlfriends, too.
Capone Barker and Ellis swing into action when a fellow office disappears and is feared murdered. Barker goes undercover with a group of Latino drug dealers suspected in the officer's disappearance, and Ellis goes to work with the missing officer's partner.
Mercy Barker goes undercover as a homeless man to solve a series of murders of homeless veterans. The case hits Ellis particularly hard because he's a veteran himself. When Rose finds out that Ellis was in the military, she tries to get him to open up to her about his experiences, but the troubled Ellis turns her down.
The Walk In Barker and Ellis work a case at a university where a Chinese spy is fronting as a professor. But finding the spy is not their only problem - an FBI agent doubts Ellis's ability and sets him up for failure.
Tilt Barker and Ellis infiltrate a high-stakes poker game to sniff out the assassin who's after an informant who's about to enter the witness protection program. Barker and Ellis have three tough jobs - protect the informant, figure out which player is the assassin, and not lose their $3 million buy-ins.
My Brother's Keeper Barker looks to take down an Irish crime family that controls a section of Chicago and is now expanding its empire to Wall Street.
Counterfeit Barker goes on the run after being set up for murder, and the FBI brings in an agent who'll stop at nothing to find him.
No Turning Back The case that's haunted Barker for his entire career resurfaces in this season finale. Barker gets a list of six names of people who were involved in the Red Gauntlet operation, and he and Ellis, with help from Todd and Conrad, must track them down before they can get to Barker.