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.

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.

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.

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.

Stella and Danny investigate when a jewellery designer is found dead, wearing the eight million dollar bra he created, and investigate the model he had shot and her bodyguard. 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.

Mac, Danny and Lindsay investigate the death of owner of a doll hospital. Stella and Hawkes look into the death of a woman with terminal cancer.

Mac, Danny, and Dr. Hawkes investigate the death of a runway model who collapsed during a fashion show. Meanwhile, Stella, Detective Flack, and Lindsay investigate a teriminally ill patient's confession to the murder of his doctor.

The life of a transplant patient hangs in the balance as the team tries to find the hijacked plane carrying the liver.

A man dressed in a superhero costume is found dead in an alley, after saving a man being mugged. Mac, Stella, and Dr. Hawkes find his clothes in a nearby phone booth. Danny and Lindsay investigate the murder of an NFL first-round draft pick, known as "Superman."

The body of a man is discovered on the Brooklyn Bridge, and the only evidence is a huge marriage proposal in lights. The CSI team works through the investigation as they learn to deal with a new medical examiner.

Three women who are dressed as Holly Golightly rob a jewelry store and injure other shoppers in the process. The CSI’s must work through the confusing investigation to hunt them down. Meanwhile Mac has to identify a mummified body discovered in an apartment building that was being torn down.

The next case for the CSI’s gets even tougher when a paintball player turns out to be the prime suspect and later goes missing the team also has another problem the evidence that should point to the prime suspect points to someone else.

After a bartender is murdered The CSI team must prove that Hawkes did not commit the murder. That only becomes more difficult when the team is pulled off the investigation.

Mac may have a difficult time solving the murder of a music mogul the sister cleverly uses a lie detector test to cover up the crime. Stella wonders if she has HIV due to an accident.

Mac believes he can fight the internal affairs investigation that is about to be started against him because of what happened to Clay Dobson. Can Mac explain what happened to the suspect he was chasing and will it be good enough for him to keep his job? Also Stella could lose her job as a CSI after a cold case is somehow connected to her.

Can the team clear a tennis legend of murder? Also Mac believes that the continuing investigation into what happened with Clay Dobson is nothing but media pressure. Can friends and colleagues help save Mac Taylor’s career before it’s too late?

After Flack makes an enormous drug bust, and locks it up at CSI, the drug lords infiltrate the building at gunpoint to get them back. Now the team must resolve the hostage situations, all the while with Mac, Stella, and Hawkes trapped inside.

As the fourth season begins the team find themselves investigating something that isn't usually on the Statue of Liberty. Can a musician's life be saved before time runs out?

While in Chicago Mac uncovers more clues about his stalker and reveals his troubled past. Meanwhile, in New York the rest of the team is in danger. The hunt is on to figure out the identity of the 333 stalker before time runs out.

Danny is devastated when a young boy he knows is killed in the midst of a bodega robbery. Meanwhile, Lindsay, Stella and Flack investigate the death of a man killed by an exploding cigar that is connected to a joke shop proprietor and another tragedy that occurred years before.

Stella's life is in danger after her apartment is on fire; she must try to save everyone in the building. The team also has a mystery to solve after finding a dead body in Stella's apartment building.

Picking up where the season 4 finale left off. The team is investigating the death of a woman named Lauren Santana whom is linked to the bank robbery. She is a friend of Flack's sister Samantha.

Also Mac has escaped the robber but the bodies are still piling up. So the team must quickly find the bank robber before he is able to get away.

The team investigates the brutal murder of a house relocator who was found dead inside a Victorian house that he was about to move from Staten Island to The Upper East Side.

In the one hundredth episode of CSI: NY Mac faces his most deadly foe yet. There is a serial killer loose in New York City killing people with the name Mac Taylor making Mac a target.

A Russian tourist is found stabbed to death and the CSIs come face to face with the frightening realities of human trafficking. Solving this case becomes personal when it directly affects a prominent member of the NYPD

Mac informs an ex-con that he served time for a crime he didn't commit, and Lindsay tells Danny "it's time" for the first CSI baby to be born.

Danny and Mac have yet to get any leads on a cop killing when Danny gets an impromptu call from a young woman who claims she's got information about the case...