The daughter of a Cuban mobster is murdered, and Jim must solve the case while preventing a war between rival mob families. Callie prepares for Ray's release from jail, and tells Jim she wants to be with him, yet promises Ray to hold off on a divorce for three months. Manus warns Jim a complaint has been filed regarding his relationship with Callie, and advises Jim to allow the family to solve their problems.
Jim hunts a serial killer from Chicago with the help of detective Samantha Harper, who Callie learns is his former lover. Manus offers Callie a job with the FDLE as a forensic nurse.
An incident at a slumber party and a missing baby are the concerns of the day---the baby is the son of the Navy recruiter found dead by the slumber party girls. Callie joins the FDLE as a forensic nurse. Jim, Callie, and Samantha navigate among the recruiter's troubled former wife, the father of a Navy recruit who blames the recruiter for his son's death in Afghanistan, and the ex-wife's young boyfriend to reach the truth.
The body of a mechanic leads to an investigation involving NASCAR; when Ray is attacked in front of Jeff, Callie considers witness protection.
Longworth's investigation of a man beaten to death in a truck stop restroom finds clues leading to a luxury rehab center. In addition to the crime, Carlo is dealing with his daughter's Quinceañera and a former colleague who needs his help. Callie and Jeff are struggling with Ray's absence
A town of circus sideshow performers becomes a town of suspects in a murder. Callie and Jim come to terms on what their relationship means. Sam considers taking a job with the FDLE.
The murder of a Haitian doctor leads Longworth and the FDLE to a pill mill and a corrupt doctor's office. Addicts have been paying big money for pain medication all of which leads to a long list of suspects.
The FDLE enters the battle between good and evil when a Pentecostal preacher is found dead in a snake pit. Longworth's investigation into the House of God eventually leads him to the Big House and a fatal case of mistaken identity. Meanwhile, Sam's departure has Callie questioning her own relationship with Longworth.
Jeff's mentor, the high school soccer coach, is found shot dead on campus.
When body parts of a Coast Guard Reservist are found in the belly of a poached wild boar, Longworth hunts the killer into the depths of the Glades. Meanwhile, Callie and Longworth decide to push the restart button on their romantic relationship.
A body is found at a popular beachside bar with a large diamond ring in his pocket. Longworth sifts through the sands of the various characters at the bar, revealing a complicated love triange that may have ended in murder. Meanwhile, Callie has some news for Longworth that will change everything.
An Ernest Hemingway look-alike is discovered adrift under a glass bottom boat with a bullet hole in his head during a "Hemingway Days" booze cruise. Turns out, the victim might have gotten caught in the middle of a family feud between bootleggers. Meanwhile, an old romance from Callie's past reappears and drops a bombshell, one that could seriously affect her relationship with Jim, the FDLE, and the hospital.
In the thrilling season finale, Callie's hospital is on lockdown when a pair of ex-con brothers take hostages. Longworth and Callie work together to ensure the safety of the hostages, but things take a turn for the worst leaving Longworth to defuse the situation before it explodes.