When city health inspector Larry Chapel is found dead in an elevator, a quick look into Chapel's home life introduces them to Chapel's recently widowed brother, Evan, and little girl Gwen. Goren isn't very surprised to learn that Nicole Wallace is Evan's fiancée and the future mother to his little girl, but Major Case soon realizes they're off the mark in who they believe the suspect is, and Goren's only hope is to get Nicole to help him trap the killer. Logan joins the Major Case squad, but isn't pleased with being relegated to the background while the other detectives solve the cases, and Deakins tries to find a partner for him.

Logan and his new partner, Barek, investigate a series of robberies in mom-and-pop jewelry stores that are escalating in the level of violence. After a home investigation leads them to a young junkie, Barek and Logan are soon led to a mother-and-son team of criminals. They soon realise that the mother is the one pulling all the strings. Logan is uncomfortable when Barek uses his past to get through to their suspect.

Prison warden William Hendry is found brutalised after he goes to drop off a large ransom payment for his wife, kidnapped years earlier by an escaped convict. Eames and Goren track down Jenny Hendry, living happily under a new name, and begin to realise that Hendry isn't the squeaky clean martyr that he's been portrayed as for years, especially once they discover that Jenny's supposed 'kidnapper' was originally hired by the warden to kill his wife.

When a cop's son is murdered by the mob, Logan and Barek realise that young Joe Long was killed by mistake, and their investigation leads them to two rival mafia families, but it isn't long before Logan begins to believe that the true criminals aren't the mobsters, but the cops on their payroll. As their investigation narrows down to one main officer, Barek and Logan are faced with the difficult task of having to force the man's daughter to turn against him to get what they want. When the officer and his lawyer bring Logan's stormy history into play, even Deakins takes pause with his decision to have Logan on his force.

After the murder of a nun in the Church, Goren and Eames investigate and realise that someone has tried to cover up part of the crime. Their investigation leads them to a young man named Eddie Roberts, who in turn inadvertently leads them to his older half-brother, Jimmy Jones, who was assaulted in a baseball field seventeen years earlier and left with debilitating injuries. Goren and Eames soon realise that the key to the nun's murder is the young woman who watched Jimmy's attack, and the only way they can get Eddie to take responsibility for his crime is to find this missing witness.

Detectives Eames, Goren, Barek, and Logan must solve a case that involves a teenage girl missing in New York City. While Barek and Logan search around for another missing girl, Eames and Goren work to uncover a mystery with a judge and his son.

The squad continues the investigation into the murder of a teenage girl visiting from Iowa. The detectives uncover the sordid family life of a local judge whose son is linked to the Iowa teenager and another victim. Goren and Logan discover that the judge is a formidable foe as they come under scrutiny.

When the body of a young woman is found by two children behind a dumpster, Barek and Logan soon learn she had recently returned from Guatemala and was suspected by the other passengers of being a drug mule. Their investigation leads them to noted plastic surgeon Dr. Christine Ensel, who has made a name for herself in recent years performing surgeries in Guatemala on people who would not normally be able to afford plastic surgery, but as the investigation continues, Logan and Barek suspect that Dr. Ensel has a lot to hide.

After Aidan Grant, an employee for a local computer company, is found dead, Goren and Eames investigate, initially believing that Grant was murdered because of a business deal gone wrong involving biometrics, lip-reading, the company Ubicool and the military, but their investigations lead them to a young man named Robbie who worked in the office opposite Ubicool. Goren soon realises that Robbie isn't fully in control of his actions and suspects his therapist, Dr. Pynchon, of wrong-doing, but Carver wants them to get the answers from Robbie no matter what they need to do.

After Joseph Sabo is found lying dead in the street, Barek and Logan investigate who was nearby that night that may have had a motive. They are soon led to Danielle Quinn, who had been blackmailing six different men claiming they fathered her child, asking for money. The detectives realise she was the one who killed Sabo, but when none of her victims will testify against her for fear of their wives finding out what they've done, Barek and Logan hit a dead end.

After Russ Corbett and his wife are found in a seedy hotel room, Russ dead of an overdose, Eames and Goren follow the trail of evidence to Bernard Fremont, a professional partier. With his beautiful blonde companions, Fremont insinuates himself into the lives of couples who don't know the city very well, then robs them blind. While investigating Fremont's past in Asia, Goren realises that he is the mastermind that turned Nicole Wallace into a murderer, and his most successful pupil.

Logan and Barek investigate after a body is found in the ocean, having fallen from an airline wheelwell. They soon discover that she is just one in a long line of prostitutes to be beaten and murdered. Their investigation leads them to a nervous airline employee, but they just don't feel he has the courage or the violent nature to commit these crimes on his own. A family connection leads them to a second suspect, with a history of both being abused and being the abuser.

Logan and Barek investigate after secret service agent Paula Kendall is found dead in her home. Suspicion initially turns to the husband after detectives realize that it took him eleven minutes after a first failed attempt to get in touch with 911, and their investigation leads them to her husband's role in a proposed Indian casino. Logan and Barek are especially interested when it turns out that the 'witness' Paula was supposed to be meeting that night had ties to a local politician, Peter Bellingham, who also had ties to Kendall's husband.

Goren and Eames investigate the death of Eric Newsome, an urban explorer who was found in a water tower. During their investigation, they learn that Eric had been looking into the files of Dr. Everett Janns, an OB/GYN who had examined his sister Nikki's boyfriend Drew's mother years earlier when she had been carrying his sister Lisa. Lisa Ramsey was born with spina bifida, and Victoria Carson was suing her primary OB/GYN, Dr. Dominic McKenna, with a wrongful life suit, charging that he did not perform the necessary tests needed to establish whether or not her child had spina bifida, which would have influenced whether or not she had an abortion.

Logan and Barek investigate after the body of eighteen-year-old violinist Laura Booth is found stuffed in a shaft, her fingers covered with cocaine and resin. Although initially they believe her death may be connected to the cocaine that some of the crew were transporting, they're soon turned on to a romantic relationship between the maestro, Julian Reinhardt, and the victim's mother, Gillian Booth. Once teethmarks are found on Reinhardt's back that belong to Laura, Logan and Barek think they may have a slam dunk on their hands until Gillian weds her daughter's supposed killer.

Goren and Eames investigate after a bridesmaid, Megan, is found dead in the cheap motel room she had been sharing with Alice, another bridesmaid at their friend Tory's wedding. The two detectives start with investigating Pete and Jayson, the two guys the women had met at Brasserie Nylorac, but soon realise that Alice's story has a lot of holes in it, and the presence of cigar smoke around Megan, a young woman who hated smoking, leads Goren and Eames to suspect that the killer had a personal connection to Megan. Their investigation soon leads them to a cab driver named Lester Summerhill, whom they soon realise is an actor preparing for the ultimate role.

Barek and Logan investigate when the deaths of two young girls seem to be connected to a voodoo-practicing nurse. Things turn interesting when it seems the young woman has placed a voodoo curse on Logan.

Goren and Eames investigate when a respected professional is found murdered in the East River, his death presumably connected to a series of gambling losses.

Logan and Barek investigate a series of home invasions that result in grisly murders and their search leads them to local foster mother Chesley Watkins who had a series of young men going in and out of her home throughout the years. One of the young men involved in the home invasions was one of her boys, and while trailing the young man, Logan shoots a suspect who was brandishing a weapon at himself and Barek. When the suspect turns out to be a cop, Logan finds himself in the hot seat, and Barek sticks up for her partner, knowing that the truth is on their side. The investigation leads to Watkins as a suspect, and Logan is forced to deal with memories from his own past as Watkins plays on the weaknesses she sees.

Goren and Eames investigate a fire at St. Gerald's which led to the death of a Church employee and soon realize that an arsonist around town is targeting churches. Throughout their investigation, they realize that St. Gerald's was the arsonist's primary target, and clues lead them to Justin Reid, who had donated $100,000 to rebuild the Church, his step-mother Regina, whom they soon learn had seduced Justin when he was only a teen, and his half-brother Glynn, who works for a clean-up crew that had worked at all the churches that were burned down shortly after they were renovated. Deakins comes under fire when an e-mail surfaces that insinuates he got Martinez (from To the Bone) to lie about the Logan shooting by getting him a promotion. The e-mail is soon traced back to former cop Frank Adair (from Season 4, Ep. 22 - My Good Name), who is doing time for murder.

Logan and Barek investigate a troubled young man named Kevin Colemar after his parents are found murdered in their suburban home. Kevin initially believes that drug dealers named Big Lennie and Ray-Ray may have done the murders, but Carson Laird, a Nassau cop, soon tricks Kevin, who cannot remember the night in question, into confessing to the murder. It all seems cut and dried, but Logan and Barek just can't shake the feeling that the kid is innocent. Deakins spends his last two weeks on the job preparing for his future.