When a teenage girl returns home from a big party night at an underage nightclub to find her parents murdered, the search for the killer leads Horatio to New York City. Before he arrives, the New York detectives, led by Detective Mac Taylor, are called out to investigate the shooting of an undercover police officer – who, it turns out, is the lead suspect in the Miami case. However, the medical examiner determines that he has been dead for 72 hours and could not even have been alive at the time of the double-murder in Miami. After further investigation, Horatio and Mac determine that the real killer murdered the New York cop, then used his ID to get to Miami, and is still on the loose.
The CSIs find three young women, all of who appear to have been brutalized in the same way. Photographs found at one of the crime scenes lead the team to a couple that had sponsored one of the victims, and the boyfriend of another victim who claims he hasn't spoken to her in weeks. But the only witness they have is one of the young women, who can communicate only through blinking.
A wealthy young girl is found to have been raped and beaten in Central Park, but only a peony leaf on her clothing can direct Stella and Flack to the scene of the rape. Worse, no DNA is found from the rape kit and the victim has no memory of what happened, making the task of finding the perpetrator a real challenge. Meanwhile, a junkie is found shot to death in an alleyway, but the bullet that killed him is missing. Mac, Aiden 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 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 belongs 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, 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 a high-class sushi restaurant.
Stella and Aiden investigate when the body of a teenage girl is retrieved from the harbor. 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. Mac and Danny investigate when a body is found in a construction tunnel for a new part of the city's water supply. However, they end up running into difficulty when the Sandhogs, a union for the tunnel's diggers, blocks many of their attempts to get information about the victim.
Terrell Davenport and Octavia Figueroa are the only survivors of a brutal slaying and robbery at a fast food restaurant that leaves Danny and Aiden scratching their heads when they can't find a suspect until they take a closer look into the life of one of the survivors. Mac and Stella investigate the death of a man who recently had his leg amputated, only to learn that there was no medical reason whatsoever why the limb had to be removed.
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 woman 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.
A game of one-on-one is interrupted by the discovery of a woman covered in blood leaning over the body of another woman who has had a stake driven through her heart. Mac soon realises the woman was sleepwalking and tried to save the victim's life, but the case stalls because she is the closest thing they have to a witness, and she has no memory of the event. Danny and Aiden investigate the brutal murder of a pickpocket whose identity they track down using information on an experimental medical trial. Money found in the victim's underwear leads the two to another pickpocket, but there is no obvious motive for Lenny Cook's death.
Mac and Stella investigate the electrocution death of a man found in a subway tunnel. Danny investigates the murder of a gallery owner whose death is connected to the mob. Aiden and Flack investigate the death of a construction worker.
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.
Mac and Stella investigate the death of Paul Montenassi, a young man left to bleed to death in the snow. The investigation leads them to another victim, Mihok Lev, who had been killed by Montenassi in a robbery earlier that evening. When Hawkes concludes his autopsy on Montenassi, he is able to reveal a sanded-off tattoo that leads the detectives to the Tanglewood Boys. Danny and Aiden investigate the hit-and-run that caused the death of Marta Santo. After discovering sperm on the woman's clothing, Danny and Aiden learn that Santo liked things rough, and their investigation leads them to an erotic massage parlor.
The body of a young trapeze artist 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 arist, 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.
Mac and Stella investigate when they find the body of Paddy Dolan, a longshoreman. Part of the body is found on a transport truck and another part back at the warehouses, but Mac encounters difficulty with the investigation when the workers put up a wall of silence against them. Aiden and Danny investigate the death of Debbie Bogda, who was found naked on the expressway, and their investigation leads them into a world of sexual games and bondage once they realise she was actually harnessed to the front of a truck.
When young gang members murder the owner of an upscale Bronx wine store, the CSIs must work to find evidence that ultimately ties someone to the crime. Before dying, the storeowner makes a statement to police identifying his attackers as young gang members. Tempers flare when the murder investigation reunites 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 misdemeanour, 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 roommate who is now missing. Meanwhile, Stella's aggressive interrogation tactics with a witness threaten her police badge.
While processing a crime scene, Danny is suddenly attacked by a suspect hiding in the victim's closet. The ensuing chase leads them to a crowded New York subway where the suspect, an undercover cop and Danny all fire shots. When the smoke clears, the team is left with a dead cop, a missing suspect and Danny under investigation for the possible murder of the officer. Mac must prove who killed the cop in order to save Danny's job. Meanwhile, Stella investigates the death of a nanny killed in a Central Park restroom.
The team examines the murder of an avid Boston Red Sox fan found dead with a ruptured spleen following a tough loss against the New York Yankees. 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.
Stella and Danny investigate when a jewelry designer is found dead, wearing the eight million dollar bra he created. Aiden begins to take the rape case she has been working on a little too personally, and is determined to stop the man before he can rape again. Hawkes gets to go into the field for the first time as he assists Mac in investigating the death of a man who liked to climb skyscrapers.
Stella and Danny discover the world of cuddle parties: non-sexual events where adults touch and hug each other. Meanwhile, Mac, Hawkes, and Flack investigate the death of a hated plastic surgeon found covered with lye with thousands of eyewitnesses during rush hour at Grand Central Station. Mac and Stella begin to assist Aiden in a rape case, but after it is learned that she broke an evidence seal, Mac must come to terms with this and work up the nerve to fire her.
Mac and Danny look into the mysterious death of a man torn apart by tigers at the Bronx Zoo, which leads them to both the dead man's meat packing plant as well as his Mafia relatives. Hawkes and Stella are left with the case of a beautiful young debutante found dead on the carousel only hours before her coming out.
Mac and his team investigate a double murder at an oil company. Hawkes and Flack team up to investigate a case about a murdered teenager who loved to spend his time behind the computer a little too much.
Mac, Stella and Flack investigate the death of a young dancer who recently won the lottery, in which they soon realise that her death is connected to Lindsay's investigation, which concerns the death of a tram driver. Danny and Hawkes look into the murder of a local fish merchant whose son attends a prestigious private school.
When a man is found murdered in an elevator, Mac, Danny, Flack and Lindsay's investigation leads them to an agency where very young girls enjoy sexual encounters with much older men. They're soon left trying to determine whether their best lead is a suspect, a witness... or the intended victim. Stella and Hawkes investigate the death of a young man found in Central Park who died from an extreme allergic reaction and learn that he had been pretending to be someone that he wasn't.
Following up from the CSI: Miami episode Felony Flight, 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.
Mac and Stella investigate a murder of a host of a high stakes poker game after a player was caught cheating and kicked out of the game. Danny and Hawkes follow the clues that lead them to solve the death of a local weather girl.
Mac, Danny and Lindsay investigate the death of the owner of a doll hospital. Stella and Hawkes look into the suspiciously sudden death of a woman with terminal cancer.
Mac and Stella work on the case of a murdered female roller derby player. Danny and Hawkes look into the murder of one of New York's upcoming crop of writers.
Danny and Stella are forced to find innovative ways to process a crime scene when Danny is trapped in a panic room with the victim, who was the only person with the security code. As a locksmith works to cut through the titanium doors, the CSIs rush to process the evidence before the victim decays further and Danny's oxygen runs out. Meanwhile, Mac, Hawkes and Lindsay investigate the murder of an exotic dancer found dead on a klieg light.
Mac, Danny and Hawkes investigate the death of a runway model who collapsed during a fashion show. Meanwhile, Stella, Flack and Lindsay begin an investigation when a terminally ill patient confesses to the murder of his doctor.
Danny, on his way home after a long shift, discovers the body of a young man on the subway tracks. Mac and Lindsay, called to the scene from separate social occasions, try to determine if the young man died after a reckless subway surfing session or if he was merely dumped on the tracks.
An assistant district attorney found dead in a graveyard leads the CSIs to a strange game being played by various people all over the city. The team also investigates the death of a woman known for her frivolous lawsuits, which leads them to a bizarre restaurant.
A young boy witnesses the death of a museum curator but refuses to tell the CSIs what he saw. Meanwhile, Danny looks into the death of an urban golfer found dead on a construction site.
Mac, Danny and Flack must race against time to save a liver transplant patient when the plane carrying the new liver is hijacked. Meanwhile, Stella and Lindsay investigate the rape and murder of a woman found in a tunnel.
Mac looks to connect the Tanglewood Boys gang to a body found at Giants Stadium, but the evidence at the crime scene seems to point to someone close to him.
The limousine driver of rock star Kid Rock is found dead. The case gets complicated when it turns out the last known person to see the victim alive was Kid Rock himself. Stella is attacked and held hostage by her ex-boyfriend in her own apartment.
Mac and Stella deal with two women who both claim to be the wife of a murder victim. Meanwhile, Danny and Lindsay investigate the murder of a young woman, dressed as a mermaid, who is found tangled up in kelp off a dock.
Mac and Danny find a Marinecorporal dead in Central Park during Fleet Week. Stella, Lindsay, and Hawkes investigate when a body burned beyond recognition, is found in a car. They initially believe the body is that of the car's owner, a male, but the autopsy reveals that the body is female. After Hawkes completes a facial reconstruction of the skull, the CSIs are horrified when they learn the victim's true identity.
Mac, Lindsay, and Flack are called to a crime scene where a security guard is found stabbed to death by a stairway. Investigating the surrounding area, however, Mac discovers a bomb. Before he and Flack can escape the building, after leading the inhabitants to safety, the bomb goes off, severely injuring Flack and several others. Amid the following chaos and involvement of Homeland Security, as well as being contacted by the bomber who threatens to bomb another location, Mac recalls a traumatic event from his Marine days when he was serving in Beirut in 1983.
The team is called in when a man is found dead on the Brooklyn Bridge after what appears to be an unsuccessful marriage proposal. Meanwhile, Hawkes, Danny, and a new addition to the team, Detective Jennifer Angell, investigate the death of a wealthy heiress in her apartment, found with pillows shoved over her hands.
The team is called in when three young women rob a diamond store dressed as Audrey Hepburn's character Holly Golightly from Breakfast At Tiffany's, leaving one man dead from accidental causes. Mac and Angell investigate when a woman's mummified body is found in a building slated for demolition.
Danny, Flack, and Lindsay encounter a rapidly-melting crime scene when a model is found dead at an ice-themed promotional party for vodka, apparently stabbed by an icicle. Mac, Stella and Hawkes investigate when a businessman competing in a marathon across Central Park is found dead from what appears to be cyanide poisoning. All the while, Lindsay and Danny try and sort out their growing feelings for each other.
A decapitated corpse is found hung upside-down in a dorm room during a party. The shirt the victim was wearing is decorated with symbols out of numerology and Greek mythology, and also contains code words that, with the aid of a witness, leads the CSIs to a bizarre website. When another brutal murder occurs with the victim wearing a similar shirt, the team realizes they have a serial killer on their hands.
Danny, Lindsay, and Hawkes investigate the murder of one of the altporn models known as the Suicide Girls while Mac and Stella look for answers in the death of a street basketball player.
Gunshots are heard during an investigation of the death of a hotel concierge, leaving the CSIs faced with another crime scene with two dead bodies and a nervous woman with a gun.
A young woman dies after she starts bleeding from her eyes, nose, and mouth while at a party aboard a subway train, leading the team to speculate that she is the victim of a biological attack. Hawkes soon realizes that he knows the victim. Across town, a wealthy playboy is found murdered in his indoor lap pool in his penthouse suite. The evidence seems to point to his last maid, who was fired two days earlier.
The CSIs are called in when a young paintball champion is found dead in a warehouse. They soon find out that his firecest rival, who he was faced in a deathmatch with, has gone missing. The case grows complicated when traces of cocaine are found in the warehouse that lead the team to an old drug bust that one of their own was in charge of. Meanwhile, Stella is concerned that she is being followed by someone.
A young girl is found murdered in her hospital room, five days after getting into a car accident which left her paralyzed and her passenger dead. Hawkes, who used to work at the hospital, has a bitter confrontation with his old boss, the hospital's chief of staff, reminding of him of why he quit being a doctor to become a coroner.
A parachute jumper meets his death when his parachute is struck by a flock of pigeons, all of which strangely end up dead beside his body. Mac, Danny, and Flack then discover the pigeons were used for racing, but when they track down the birds' owner, they find him murdered inside their pigeon coop. Stella, Lindsay, and Hawkes investigate when the father of a girl celebrating her Sweet Sixteen is found dead inside the Mercedes he bought for her.
The CSIs are called in when a bartender is robbed and shot. When the police capture a suspect matching a witness' description, the team is stunned when the suspect is Sheldon Hawkes. Despite being pulled off the case and being reassigned to one involving a junkie found dead in an adult bookstore, the team tries clandestinely to exonerate Hawkes and find the real culprit.
Mac and Hawkes have a problem when they find out that the family of a murder victim are all deaf, so they have to find a new way to catch the killer. Danny and Stella investigate the death of a competitive ice skater and wonder if she had been stalked. More information is given on Lindsay's horrifying past and what led her to become a CSI.
A well-heeled man is found dead in a vacant apartment, but the evidence suggests that the victim may have been killed by someone he kidnapped. In Central Park, a man's body is discovered stuffed in a shopping cart. The probe reveals the dead man was part of a bizarre race that uses shopping carts and that his team was sabotaged by other participants.
A female impersonator who performed at a party in a ritzy hotel is found dead in a men's room stall, drowned in the toilet. The investigation reveals the victim confronted a Congressman at another hotel event shortly before being murdered. Across town, a man's body is found inside of a city salt truck. Lindsay returns to Montana to testify as the only witness in a multiple-homicide trial.
Mac and Hawkes investigate the death of a college student and learn of his involvement with a secret society. Danny and Stella look into the death of a security guard at a lavish store and eye a professional shoplifter as their prime suspect. Featuring guest star and music from Nelly Furtado.
When a music industry mogul is murdered in his high-end penthouse apartment, Mac, Stella, and the team must rely on the crime's only witness, the victim's sister, to solve their case. Stella is injured while processing evidence, which has greater implications than she had bargained for. Danny works to figure out how a woman ended up dead in a bathtub.
