The team finds three young women, all of whom appear to have been brutalized in the same way. The only witness they have is the surviving young woman, who can communicate only through blinking. Photographs found at one of the crime scenes lead the team to a couple that had sponsored one of the victims, and the boyfriend who claims he hasn't spoken to her in weeks.

After mounted officer Valasquez is shot down in the park, Mac goes looking for the bullet that killed the officer only to learn that it is lodged in the horse's spine and cannot be removed without being fatal to the horse. The investigation leads them to a local street vendor, but stalls when the D.A. asks Mac not to do anything to risk the horse until after the woman who donated it has a chance to say goodbye. Aiden investigates the body of a young man, Lenny Starks, who was found face-down, dead in the street. Aiden traces the young man to a local pizza parlor where she faces intimidation from the bookies who use it as a gambling front.

Mac, Aiden and Flack investigate when Elaine Curtis is found dead at a dog competition, a knitting needle sticking out of her chest, and no shortage of suspects ranging from judges to trainers to contestants. Stella and Danny investigate the death of bicycle messenger Michael Starling, but the crime scene may have been anywhere along his route.

The detectives investigate a murder at a grocery store that is also connected to the death of a young man with the tattoo "Tanglewood" on his back. A third case involves a woman who was killed in a hit-and-run auto accident.

The team's investigation into the death of Hannah Bloom, who died at her own wedding, is put on hold when her father refuses to allow them to perform an autopsy until after his daughter's body is blessed by a rabbi. Danny and Mac turn their attention to the woman who trained the doves who were supposed to be released, but cannot tie her directly to Bloom, who died from formaldehyde poisoning. Stella, Flack and Aiden investigate when a hand is found deep underground, and soon realise that the dead man, Rick Amadori, chewed off his own hand. It seems like a slam dunk when the son of a man Amadori killed three years earlier confesses to the crime, but things aren't as easy as they seem.

A woman's death leads our detectives to a school for sexual fetishes such as bondage and spanking.

When young gang members murder the owner of an upscale Bronx wine store, the CSI’s must work to find evidence that ultimately ties someone to the crime. Tempers flare when the murder investigation reunites Detective Flack with his long-time mentor and friend Sergeant Gavin Moran, who was the first to arrive at the crime scene. Meanwhile, Danny and Aiden investigate the death of an influential movie producer found dead on the canopy of his Chelsea apartment building.

When the chief investigator of a controversial report documenting corruption within the NYPD is gunned down the day before his findings are published, Mac and Stella must find the killer, launching a massive search that makes every officer listed in the report a suspect. Meanwhile, Danny and Aiden investigate the murder of a gypsy cab driver.

(Crossover episode with CSI: Miami, Season 4 Episode 7.)

Horatio Caine follows Henry Darius to New York so that he can keep his promise to a young boy in Miami, but by the time he and Mac are able to locate Darius he has disappeared again, leaving behind six more bodies. A link to the younger sister of one of the victims who was also Darius' hostage turns out to be a dead end, but Mac and Horatio soon find the connection between Darius and his hostage, leading them to a psychiatrist who had treated both.

Danny is on his way home after a long shift and finds Randy Williams subway surfing. Mac and Lindsay arrive on the scene and begin to wonder if Randy Williams died from riding on top of the subway. His death is even more suspicious after they examine the body more closely.

Mac receives a phone call confessing to an old murder before the caller commits suicide. The call leads the team to a football stadium to uncover a body and they learn the suicide victim belongs to the Tanglewood gang. They also find a cigarette that puts Danny's job on the line after his DNA is found on it.

Stella and Danny investigate the death of a businessman who used the services of an expensive call girl service.

Mac and Lindsay question Kid Rock because he was the last person to see his limo driver alive when the driver is found dead in the alley just before Kid Rock’s encore performance concert.

The CSI's handle to puzzling cases; Carensa is a young Suicide Girl who at 17, wanted a change of scenery and to become a Suicide girl, at 18 she gets her wish only to lose her life. Chopper, a rising street basketball star, a homeless man trying to change his life for the better is killed and leaves a painful trail of blood which leaves Mac to figure out where and how he died.

The CSI team has a problem after learning the family is deaf: now they have to find a new way to catch the killer. Meanwhile, more information is given on Lindsey's horrifying past and what led her to become a CSI.