With his life in shambles, Malcolm investigates a new case, while seeking to take care of his sister and chase away a secret that might have fateful consequences.
Malcolm is forced to confront his own demons, while investigating the murder of a priest. Jessica breaks up with Gil. JT’s fears of other officers’ giving him a hard time come true, as a result of the incident he had with the racist cops.
While investigating a murder at his alma mater, Malcolm is haunted by a disturbing memory from his school days. JT’s wife gives birth to a baby boy. Jessica broods over her breakup with Gil.
As Malcolm’s father witnessed the alleged murder of a fellow inmate, Malcolm is compelled to enlist his help. Ainsley starts to piece together some memories, which causes her to have qualms about Malcolm.
Malcolm sets out to catch the” Debutante Slayer", a serial killer, whose victims are students at a girls’ school, only to be obstructed by Ainsley’s intrusion. Martin receives a visit from Jessica, who considers taking Ainsley to Europe.
Following an accident, Malcolm finds himself living in a world created by his own imagination, where he comes from a normal and happy family, and enjoys a loving relationship with Dani, but he soon realizes there’s something off.
While still at odds with Ainsley, Malcolm takes on the investigation into the murder of a plastic surgeon. Birdie, Jessica’s sister, shows up unexpectedly. Martin starts working as a janitor in the infirmary, where he meets Dr. Vivian Capshaw.
Malcolm meets Europol profiler Hoxley, who claims there’s a connection between Endicott's murder and the Major Crimes’ case; meanwhile, Martin gets closer to Vivian.
Even with Gil’s urging that he take time off work, Malcolm takes on a new case, whose victim is a member of Edrisa’s group of vigilantes called the “Killabustas”, which targets serial killers. Jessica enlists Gil’s help with writing her memoirs.
As Malcolm and Dani question an agoraphobic witness at his home, the latter seems to discern Malcolm’s feeling for Dani. After causing a lockdown, Martin breaks out of prison, with Friar Pete and his disciple.
While disturbed by the thought of Martin being on the loose, Malcolm sets out with the NYPD to find the fugitives, but several leads prove futile.
When Malcolm is taken off the case of a serial killer, he goes rogue, taking the law into his own hands, whereupon dire consequences ensue.
While the NYPD is on the hunt for a serial killer known as the “Woodsman”, Martin, in an attempt to redeem himself, embarks with Malcolm on a fateful mission.