The two young owners of a city bar are gunned down after hours and another man is wounded in the attack, which was allegedly committed by a masked gunman. Meanwhile, Calleigh's dad announces he is now a public defender and needs her help with a murder case in which a woman allegedly stabbed her boyfriend to death in his car with a screwdriver.

An anesthesiologist who worked in a beauty clinic is discovered swinging from a rope in his two-story condo, but the investigation points to murder, not suicide. The case intensifies when it's learned that the doctor lost a patient the week before during routine plastic surgery and that the victim's husband believes she was killed.

A cigarmaker is found in his store tied up, beaten, mutilated, and murdered with a chaveta, a cigar-making tool featuring a rounded blade. The investigation leads Horatio to a group that helps Cuban refugees. Across town, a 25-year-old man is gunned down while withdrawing money from an ATM, but the motive doesn't appear to be robbery since the cash he withdrew is left behind.

The CSIs must find the killer after a young woman is pushed in front of a moving bus. Alexx finds a bruise shaped like a hand imprint on the victim's back, proving that she was pushed in front of the bus, and her boyfriend, Jay Seaver, is the prime suspect. When one of Jay's office rivals also turns up dead, Jay reveals that he has a psychotic stalker, Claudia, who he thinks might kill to please him. However, when Jay hires a lawyer to protect Claudia, Horatio suspects that Jay may be more involved than they thought. Later, a man's body is discovered down an elevator shaft in a nearby building, and there is evidence to link the victims to a common killer. Meanwhile, Calleigh's father seeks her help when he fears that he may have killed someone after a night of drinking, and Horatio assigns a new CSI, Ryan Wolfe, to the case.

The wife of a famous baseball player is brutally killed in her home and her philandering husband is charged with the crime. The jury on the case, as well as the accused and his defense, visits the house to examine the crime scene, but when the lights are dimmed, as they were when the victim was killed, and then turned back on, the ball player is found dead with a meat clever in his back and a note that reads "guilty." Now, as Horatio and the team find that the husband's defense team tampered with the crime scene, they must examine the evidence to find the couple's killers. Meanwhile, Horatio gets a call from Yelina, who tells him that her son, Ray, Jr., is missing.

The CSIs must investigate when a pedestrian is killed after a man falls from a building and lands on him. Horatio and the team find that the victim found on the sidewalk is not the same man who fell from the building, but the unfortunate person he landed on. The CSIs discover that the fallen victim is in possession of a sex DVD involving a top Miami criminal judge and a woman with a sordid sex life. When the woman is found dead, the team must delve into the complicated personal lives of those in Miami's judicial system in order to find the killer.

Someone uses a laser light to blind a pilot and bring down a jet, which carries $1.2 billion in checks to be delivered to banks on the eastern seaboard. The crime scene evidence reveals a victim, a young fundraising socialite, who was inside the plane but killed prior to the crash. Now, although the team has little to work with since the victim's wealthy family is opposing an autopsy, Horatio must follow the money trail. Meanwhile, Calleigh works on the case with her ex-boyfriend, Detective Hagen, and their romantic history could cause problems for both of them.

An axe murderer on death row is given a stay of execution just moments before it was to take place, on the grounds that there may have been tainted DNA analysis used at his trial. Now, without using any DNA evidence, the team must race against time and reexamine all of the physical evidence in the case, just as they get a call on a new double murder that looks suspiciously like the case they're working on.

The search of a missing 17-year-old girl, whose trip to Miami turns into an ongoing nightmare.

(Crossover episode with CSI: New York, Season 2 Episode 7.)

A crossover episode that concludes on "CSI NY" begins with a convicted serial killer who escapes after sabotaging an airplane that was flying him from New York to Miami, where he allegedly buried a body. After fleeing the crash site, the man goes on a killing spree and abducts a college student. Mac Tayor arrives to help Horatio track the killer since Mac originally arrested the man in New York.

A drug lord is gunned in his Coconut Grove mansion and a suspect arrested at the scene claims he sells marijuana to Delko. Stetler, from Internal Affairs, investigates and the case quickly gets personal when Horatio gets involved. As for the shooting, the CSIs learn that two gunmen may have been involved. Also, Calleigh makes a major decision concerning her job.

When evidence shows that a series of murders is linked to organized crime, Horatio and the team are instead lead to a pair of film students who have screenplay that contains the details of the crimes.

Alexx’s DNA is found throughout her neighborhood where she is suspected to be responsible for the death of a convicted child molester. The CSI team soon learns that mindset of the neighborhood could lead to any of community wanting the man gone. The team must find out who the real killer was to clear Alexx.

After a man is found not guilty of his wife's murder the CSI team finds evidence to the contrary.

The CSI team must try to find out who is trying to kill a young couple who are released from prison. The couple was made out to be “media darlings” and soon find that not everyone though of them as darlings. Calleigh must work with her ex-boyfriend to help solve the case.

A cruise ship that is docked in Miami is the scene for a double murder. The team investigates the long list of potential suspects but soon find that the list is dramatically decreased when the CSI's find a large amount of money is missing from the victim's stateroom. Horatio and Marisol's relationship evolves.

The CSI’s investigate the murder of a male model and have to figure out the inner workings of the modeling world in order to find his killer.

After Nick is found to have been killed with all the evidence pointing to Natalia as the killer the rest of the team has been sidelined by the Internal Affairs investigation. Horatio with the help of the night shift lab and Calleigh’s ex-boyfriend have to find the evidence to clear Natalia.

A truck carrying weapons that were confiscated from previous crimes are now back on the streets of Miami. An old enemy of Horatio's puts the lives of two CSI's in harms way after a confiscated missile is launched into courthouse allowing Clavo Cruz to escape during his arraignment and injuring one CSI and the fatality of another CSI.

After a wealthy businessman is killed at a charity event the CSI's first suspect his wife who was hosting the event. The blood evidence is thought to belong to the wife or her two secret twin sisters but leads the investigators in another direction after the victim is not who they thought he was.

After the murder of a suspected carjacker the team discovers that he may have been involved with a formidable drug lord and was suspected of drug running off Miami's shores.

The investigation into a runway model's death leads Horatio to his son and his nemesis.

Deadly jellyfish are used as a murder weapon, and a mysterious woman from Jesse's past returns.