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.

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.

Barker and Ellis are tasked with keeping a top nuclear physicist alive and bringing her to the Nuclear Regulatory Commission to testify on a case. Meanwhile, Rose pays Ellis a visit at his apartment.