Immediately following the previous season finale, the team is investigating the death of a woman named Lauren Salinas who is linked to the bank robbery. She turns out to be a friend of Flack's sister Samantha. Also, Mac has escaped from the robber who gave his name as Joe, but the bodies are still piling up. So the team must quickly find "Joe" before he is able to get away.

When two people turn up dead with radiation poisoning, it sparks an urgent investigation before it turns into a deadly outbreak in New York City when it's tracked down to a book at the NYC Library.

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Note: Maroon 5 made a guest appearance in this episode.

When an Air Marshal turns up dead on a flight on which Mac is a passenger, the victim it turns out, isn't a Marshal at all. The real Marshal was killed earlier and his ID stolen. Meanwhile, Stella prepares for a baseball game during which the teams are made up of police against firemen; one with whom she is very friendly.

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Note: The Who reference: Mac uses the expression "the song is over" to let the perpetrator know that he has found out the truth about the murder.

When a prominent journalist named Ann Steele turns up dead at a street party, the investigation leads the team to a life-size silicone doll company. When Mac and the team close the case, it is revealed that Ann Steele had a flash drive on which she kept several damning secrets about several city officials and other prominent people, but at the end of the episode, the flash drive is shown to be stolen by an unknown person.

When an archaeologist ends up dead in a alley, it turns out he wasn't who everyone thought he was, and was the owner of a rare Greek coin. When Stella is linked to the person who took the coin off the body, her life is threatened.

The team investigate three separate murders, but find that the three victims were all drug dealers who were due to testify in court, and that the week earlier they tried ratting out another drug dealer in exchange for freedom, as well as attacking the only witness to their crime. Meanwhile, Adam's job is at risk.

When a dead man is found in a cellar, the rest of the crime scene is on a barge floating upriver. The team finds more than they anticipated when delving into the man's life. Meanwhile, Stella gets a threatening phone call about a previous case and Flack encounters problems caused by his sister's reckless behavior.

For the 100th episode, a series of murders are linked by the fact that all the victims are named "Mac Taylor". The New York team struggles against time in order to hunt down this killer before the worst happens.

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Note: Chris Daughtry and Rumer Willis guest star in this episode as two of the Mac Taylor's.

This is told in a flashback by Danny to two unseen persons about an unidentified body found inside a crushed car. The team must put together the bones to try and figure out who and how they died. Though initially unsure of wanting to tell him or not, Lindsay reveals to Danny she is pregnant when he sees her at a clinic the victim had been going to.

When an armored truck is robbed and a guard killed, the team finds themselves hampered by a strange energy field that appeared at the time of the incident. Danny proposes to Lindsay as they continue to explore the future of their relationship, but she turns him down stating the circumstances are wrong. Mac is questioned by the FBI about the disappearance of Ann Steele's flash drive.

A murder happens during a strange Christmas dinner party involving "mouse brains" and "cod liver oil" of an up and coming handbag designer. Meanwhile a store owner turns up dead in his shop with a broken neck. Ella McBride, the daughter of the victim in "Dead Inside", returns in effort to seek time with Mac, and appears to be infatuated with him, so much so she created fake evidence to see him, and after receiving an angry visit from Mac, later tries to commit suicide from being unable to deal with being alone.

A woman is found dead from an accident at a wedding dress sale, but she ends up connected to a woman found dead in a bathtub who was raped. The bathtub victim ties back to Hawkes' ex-girlfriend, who was raped eight years earlier, causing Hawkes and Mac to clash over the case.

After finding various body parts scattered around the city, the CSIs discover they belong to a wrestling coach at a prestigious NYC high school. The case takes a dramatic turn when Mac and his team examine the coach's computer and discover he emailed a provocative photo of a young boy to students on his wrestling team. Flack is suspended by IAB, following the death of a suspect who was in his custody.

Two separate cases become one when a man turns up dead and a young woman is missing. They turn out to be connected to a sex-slave-trafficking ring in the city. Flack is back on duty after being cleared.

Stella's date is interrupted when the body of the deputy mayor falls from the ceiling at a charity fundraiser. Mac takes on Robert Dunbrook, an influential wealthy man who runs a paper. The blue flu causes problems.

A buzzard flying over Manhattan drops a human eyeball into Stella's coffee, and the team searches for the rest of the body. Meanwhile, Mac visits Ella McBride.

Adam is injured during a game of street hockey when a car bomb goes off killing a woman. The investigation leads to an environmental terrorist group. After talking things through with Mac, Danny takes Lindsay to City Hall under the guise of meeting some friends, and with Stella and Mac as witnesses, the two marry before Lindsay leaves for Montana for a visit.

The wife of a former ME, Dr. Marty Pino, is found dead and a white powder near her body helps the CSI team track her killer. The team discovers that the powder is actually heroin made from human bodies. Meanwhile Stella and Angell continue their search for the killer of the rat fisherman.

The team has to figure out who killed the chief of a Native American tribe and why. Danny spends the time running boy names through his head and past the rest of the team, though Stella thinks they're having a girl. At the end he receives a text message from Lindsay who is still in Montana, saying they're indeed having a girl.

A voice coach is shot dead, and misleading and planted evidence leads Stella to theorize the killer may be a student at Chelsea University, due to a past lecture she did there. The case takes a baffling turn when it becomes apparent that victim wasn't so much a victim at all. Katharine McPhee guest stars as Odessa Shaw / Dana Melton.

Robert Dunbrook pushes a man through his high-rise office window. The team has to figure out what happened to the body, all while the case takes many twists and turns along the way.

A jewelry auction takes a deadly turn after one of the appraisers is shot. The case requires the team to try to understand the Holocaust. Mac learns how one member of his family experienced it. Ed Asner guest stars, and earned a 2009 Emmy nomination for his performance.

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.

A man is murdered during a theatrical performance with everyone watching. Stella gets in big trouble when Mac finds out she disobeyed an order and she travels to Greece.

Detective Angell is murdered after a deadly group of kidnappers snatch Robert Dunbrook's son while he is being escorted to court. The team are able to find the evidence and rescue the son and use deadly force on her killer. Later, as they salute Jess in a bar, a drive-by shooting threatens the life of another member.