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.
Junkie Jordy Thompkins was shot dead in an alleyway, but the bullet that killed him is missing. Taylor and Hawkes soon realise that a rat may have eaten the bullet, and finding the rat leads them to a robbery that occurred earlier that day. After Robin Prescott is found raped and beaten in Central Park with only a peony leaf on her clothing, Stella and Flack have the daunting task of trying to find the man who raped her, but Prescott has no memory of the crime.
After a skeleton is found on a tour bus and turns out to be over a decade old, Mac and the team use the backpack they have found to track the belongings to a young man named Aaron Moreland, only to learn that the body they have cannot possibly belong to him. By tracing the victim's shirt, detectives are led to a youth center worker who claims not to remember the boy, but is hiding an old secret of his own.
On the very night that he wins a D.J. competition, DJ Banner is found dead in an alleyway outside the club where the contest is being run, prompting Mac and Flack to investigate not only the club but also Banner's primary competition, who was jealous that his girlfriend's voice was part of Banner's act. Stella and Danny investigate the death of fashion designer Deborah Gayle, found face-down in the pool at her apartment by her assistant, who isn't concerned by her boss's demise. An autopsy reveals that the cause of death was poisoning by tetrodotoxin, a poison found in blowfish, which leads Stella and Danny to Fuqua Sushi.
Stella and Aiden investigate after finding the body of a teenage girl in a creek. They soon realize that she was a middle-class girl attending a fancy school who was trying to make it seem like her family had more money than they did, and trace her movements to a nightclub. Mac and Danny investigate when a body is found in the tunnels without any protective gear on, and end up running into a brick wall when the Sandhogs union blocks many of their attempts to get information about the victim.
Two cases. One involves multiple homicides at a restaurant and the other starts with an amputated leg found in a dumpster.
When the charred bodies of two men who had been robbing a Chinatown bank are found, the entire team investigates the crime, which leads them to Doris, the missing infant of the bank's manager. The team realises that Joanna Cho assisted with the robbery out of fear for her daughter's life. Mac and Stella finally manage to track down the third robber, only to find him lying in a pool of blood, with a trail of bloody baby handprints leading away from the body.
Danny and Mac investigate after a briefcase belonging to Luke Sutton is found left in the NYMEX with a bloody note inside. Their investigation into Sutton's activities lead them to Nick Lawson, whom Sutton had been investigating for illegal trades, but who swears he had nothing to do with his disappearance. Stella and Flack investigate the death of Trina Rolston, a young pregnant women who fell to her death from the roof of a church. With Hawkes help, Stella realises that the body was thrown off the roof to mask the true cause of death. The detectives soon realise that their two cases are connected.
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 and Stella investigate the murder of a woman who was stabbed in the heart with a wooden stake. The police arrest a woman who was kneeling over the body with blood on her, but Mac isn't convinced that she committed the crime.
A young John Doe, nicknamed 'Slick', is found lying across the rails of an underground subway. At first, he appears to have died from third-rail electrocution, but an autopsy suggests that he may have met his end by other means of electrocution. Meanwhile, Leo Whitefield is found shot dead at close range in a gallery he owns, with no sign of break in or theft, and a construction worker turns up with a fatal injury to the head.
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 body of a young contortionist is found folded into a box on Coney Island, leading Mac and Stella to the circus where they find themselves embroiled in a real-life Romeo and Juliet story between the dead contortionist, Lukas, and a trapeze artist, Anasuya. Danny and Flack find a woman's body in a laundry chute and learn that she was actually the former sorority sister of the woman who lived in that building, and turn their suspicion to the abusive husband the woman was hiding from.
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.
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.
When the body of a young woman is discovered at a laundry facility, the bed sheets she is wrapped in lead Mac and Stella back to an upscale New York hotel that houses diplomats from around the world when the United Nations is in special session. Meanwhile, Danny and Aiden investigate the death of a homeless man found dressed as a human statue. By all accounts, the prank is deemed a misdemeanor, but Danny decides to delve further and his refusal to stop the investigation puts him at odds with Mac.
When a college student is beaten, shot to death and his apartment ransacked in what appears to be a drug-related hit, the team must track down his killers. After examining the evidence in the murdered student's apartment, the team finds traces of pure, unprocessed heroin and discovers that the victim had a female roomate who is now missing. Meanwhile, Stella's aggressive interrogation tactics with a witness threaten her police badge.
A nanny is found dead near a park while Messer is in trouble when he may have shot another police officer.
The team examines the murder of an avid Boston Red Sox fan found dead with a ruptured spleen following a tough loss against New York. Danny must put his baseball skills to the test to piece together the evidence as the CSIs try to find out how and why he was murdered. Meanwhile, after testifying in a murder trial, Mac is confronted by the defendant, Quinn Sullivan, who questions the validity of the evidence. Mac is torn between trusting science or his desire to help a man facing jail time who swears he's innocent. Also, when a truck kills a barely clad woman early one morning, the team investigates why she was running through the streets and from whom.
While Mac dines at his local breakfast spot, a gunman opens fire, leaving a waitress critically injured and a man dead, and Mac having to choose whether to chase after the suspect or save the life of the young woman. Meanwhile, before the chaos, Mac was approached by a shy patron who awkwardly engaged him in conversation. After feeling that he saved her life during the shoot out, she asks him to join her for a drink and Mac must decide if he is ready to start dating after his wife's tragic death.
