Maverick FBI agent Charles Barker reluctantly takes on rookie agent Ellis Dove and goes undercover to find out about an illegal weapons ring and bring it down. Ellis is approached by senior agents to prove that Charles is a dirty cop but he refuses.

Ellis is re-approached to gain his co-operation in bringing down Barker but he refuses again even though they provide him with evidence. Meanwhile he tries to assist Barker in breaking out drugs baron Jimmy Casserly from police custody so that they can do a drugs trade with him in order to gain better evidence and re-arrest him but they find that an ex-police lieutenant has a person vendetta against Casserly and goes out of his way to hinder Barker. Elsewhere, Ellis finally gets to go on a date with Rose.

Charles goes undercover to bring down Romanian Roman Petrescu who is involved in human trafficking but who pleads diplomatic immunity anytime the FBI get close. Meanwhile, Ellis becomes involved with one of Petrescu's prostitutes, Nadia, and tries to locate her son who was sold by Petrescu previously. Elsewhere, Ray continues to pressure Ellis into bringing Charles down.

Ellis's brother William rolls into town after spending 7 years in jail and promptly robs his house of electrical equipment. Meanwhile, jeweler Susan Redman's son Matt is infected with a deadly virus and she is ordered to take $10 million dollars of jewels to a drop-off at Millenium Park. She follows their instructions but Baker only allows her to take half the jewels so that they hold to their deal of providing the antidote for her son. But the jewel thieves have Susan's house watched and attack her when Baker leaves and take the remaining jewels. Baker and Ellis ...

Barker and Dove are asked to protect nuclear physicist May Nan Nhung after five FBI agents are gunned down trying to protect her and are asked to get her to a NNSA hearing where she is to testify.

Ellis goes undercover as a rogue army veteran at a security company to locate FBI agent Frank Oland who has gone dark for six months.

Ellis goes undercover at Chicago PD at the same time that Barker re-assumes his old identity of 'Apache' to enter a crime gang who may have information on the disappearance of a rookie cop. Barker finds out that DEA agent Fred Lopez is also undercover in the gang and going by the name of Capone and has been there for four years. Is Capone trustworthy or has he gone dark for too long?

Barker goes undercover as a homeless marine vet to try and find out who is killing young homeless vets. Ex-marine Ellis tries to gain information from the VA Hospital Marine records room on the dead marines.

Barker and Dove go undercover at a Chicago University to try and expose Dr. Warren Shelby who is believed to be selling US defense intelligence to the Chinese. But uncovering evidence is not as easy as it seems.

Ellis and Barker go undercover at a high stakes secretive Texas Hold Em Poker game to protect a protected whistle-blower and prevent him being assassinated. Barker finally tells Ellis about his past involvement with the Red Gauntlet project.

Ellis goes undercover as a crazy drug dealer/con-artist to infiltrate the Doherty Brothers and bring them down whilst Barker goes at them from a business point of view. Meanwhile, Barker pursues ex-FBI agent Gordon Freed and who he suspects of being involved in Red Gauntlet much to the horror or Ellis who then witnesses Freed being blown up in his car.

Barker goes on a buy to get hold of stolen plates but whilst there his contact is shot dead. Although Barker was miked up, Ellis only heard what sounded like Barker was going to kill the contact. However, when Ellis gets to the meet Barker tells him the contact was taken out by a sniper. Barker then realizes he was set up and goes on the run. A new investigator, Robicheaux, is brought in to track down Barker and Ray is re-assigned. Ellis and Conrad work to try and prove Barker's innocence but they are running out of time as Robicheaux steps up the pressure. Ray ...

On trying to leave their safe place Ellis, Barker, Conrad and Kirby are attacked by a sniper and Kirby dies. Barker & Ellis escape and go about trying to find out who the final name on the Red Gauntlet list is - a man named only as Viper. They find out that the little girl that Barker thought had died in Macedonia had actually survived and was living in Chicago. They find her and use her as bait to bring out Viper through the help of Assistant Director Paulson. Conrad and Paulson ask Barker to come in and clear his name but Barker is suspicious and sets a meet with ...