Season 6

When Dana Hughes comes into the station to report to Mickey that her estranged husband murdered two hookers three years earlier, they investigate, and when the young woman is beaten, Mickey blames herself because she warned the husband to stay away from his wife. As the case goes on, Dana brings in more and more evidence against Wayne, but what Mickey doesn't know is that someone is pulling all Dana's strings. After modeling for the cover of a local magazine, Ali considers a transfer to Ottawa, where she would be working in a joint American/Canadian anti-terrorist task force. Dan forms a partnership with his uncle so he and Vanessa can go with her, but Ali's mother's past is going to stand in her way. Nicco is forced into a meeting with department psychiatrist Leanne Walker in regards to the death of André, the pimp of a young hooker named Billie that Nicco had gotten involved with and helped clean up her life.

While Mickey moves into her new position upstairs supervising all the departments, Ali takes over the case of some recent murders at a massage parlor.

Harper can't let go of his obsession with Viveca Wells. He is convinced that she murdered her last husband, and when he learns she's engaged to be married again, he tries to warn her fiancé, Richard, who tells Harper that he knows all about her past, and he's okay with it. While researching the case with Ali and trying to fight his own attraction to Wells, he learns that Richard has been the man in her life all along. Nicco is upset because in the six weeks since he's been off of suspension, he hasn't worked a single case. Ali finally throws him a bone by having him interview a prospective witness in the case of a racially motivated murder and while Nicco gets the man to ID the suspect, he's not happy with it.

The squad gets involved in the world of street racing.

A murder hits close to home for Pawlachuk.

The murder of gay-basher Ken Reegan on Davies street prompts the squad to re-open the three-year-old murder of another gay-basher, Terrance 'Tron' McLean. Nicco and Len connect with homicide to investigate the case, and Len can't keep his personal prejudices out of the case, which involve working with a gay officer, Luke Darling. Mickey uses the department's new computer toy to help Ali with a 10-year-old arson case. It eventually leads Ali to Boris Delgado, a former troublemaker who found religion after the first fire but was unable to escape his past.

Nicco take the lead in solving the case when Mickey lets him take charge, they find the criminal wearing a overcoat.

When Ali is on her way back from a routine prisoner transfer, Winslow accidentally crashes the car (somewhere off highway five between Clearwater and Little Fort), leaving Ali and himself relying on the prisoner they're transporting, Paul King, who is accused of the brutal murders of two men. Ali and the prisoner both beg Mitch to uncuff Paul so that he can help them (Ali has a spike through her arm and Mitch has suffered heavy internal injuries), but Mitch absolutely refuses. When Mitch finally dies from his injuries, Ali begins to talk to the prisoner, who maintains his innocence in the murders and swears that he's only out to save the environment.

Years ago, Pierre Martin was convincted of murdering Randall Bettinger, but suddenly Bettinger turns up alive and well, making Len, who had busted the case, look very bad. Within 48 hours though, Bettinger is found dead for real, and Casey brings in both Nicco and Len to work the case, and each uses their snitches to help prove who murdered Bettinger. Mickey gets pulled in when the murder of 6-yr-old Jeannie Yan is reopened after nearly ten years, because the girl was the first dead child she ever saw. She asks Ali to investigate, and when Ali begs off, Mickey begins doing some detective work of her own.

Ali and Len re-open the case of a corrupt stockbroker, Jack Dolan, who had stolen millions from his clients. When they begin questioning the clients, they learn that Jack and his then-wife Arlene were members of a club of swingers. Originally they look at jealousy as a motive, but no one seems to have been angry about any of the relationships. Len also finds himself interested in the lifestyle of a swinger, which Wanda shoots down immediately. Nicco is finally finished his counselling sessions with Leanne, and when she calls him to her home he goes over and spends the night. The next day Leanne starts talking about their 'relationship', and when Nicco tells her she's moving too fast she accuses him of using her for a one-night stand.

When Ali hears that suspected killer John Watts is about to be extradited for trial in Texas, she's determined to get him convicted in Canada of the murder of Gus Johansson to save him from the dealth penalty, which she does not agree with. When Ali and Agent Mitchell (who is there to extradite Watts) try to question the suspect, he grabs a cop's gun and holds Ali hostage. Nicco is accused of sexually assaulting the police psychiatrist, Leanne Walker, but maintains his innocence to Andy because what they did was consensual. When he tries to talk to her, she makes it clear that if he wants her to drop the charges, she has to come back to therapy with him. Mickey agrees to check an apartment for Christine's replacement, Denise, and learns that the building has had a large number of rapes recently.

When Nicco investigates the death of a female tree planter that took place thirty years ago, his best suspect is a well-known humanitarian Ian Northby, and Nicco soon begins to regret getting involved in the case, and finally realises that he doesn't belong in the Squad, but back on the force. After having an affair for months, Len gets antsy when Sonia gets involved in an undercover prostitution bust. She promises to quit if he will leave Wanda for her. He finally does, just as Sonja is being injected with a massive dose of heroin by the American pimp she's investigating. At the urging of the daughter of convicted murderer Abdul Rhaman, Ali agrees to look into the crime he was convicted of, the murder of Khallid Fulani. When she starts searching, she learns that Fulani never truly existed, and C.S.I.S. has seized all the files.

Nicco is finally back on general duty, and his first major investigation involves a missing girl named Mimi whose mother has been searching for her. Ali continues to meet roadblocks in her quest to learn who truly killed Khallid Fulani, and makes a decision that will change her life. Len is determined to find Sonia's killer no matter what, and finally tells Wanda the truth about the affair.