Horatio is quick on the scene when an armored truck carrying $3.2 million is robbed in a daring downtown heist. During the holdup, the driver is killed and Horatio guns down one of the two thieves. The other escapes with the loot, but the money turns out to be counterfeit. The team must figure out what happened to the bank's money before it was replaced with fake bills. Making the day even worse for Horatio, Yelina spies him with his niece and assumes the girl is his illegitimate child, not her own late husband's daughter.

A police officer collapses and dies after pulling over a car, and the investigation reveals he was murdered. Horatio grows suspicious when Internal Affairs gets involved in the case, leading him to believe that the killing wasn't a random crime. Meanwhile, Calleigh aids an abused woman who is living with one of the suspects in the probe. Yelina begins dating Horatio's nemesis – who is heading up the Internal Affairs inquiry.

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

The CSI's are called out to investigate the murder of a young woman who was about to sign her divorce papers. Soon the husband turns out to be the ideal suspect. The only strange thing about the case is the murder weapon: a nailgun. The case becomes complicated when one of the CSI's is attacked when he returns to the crime scene and ends up in hospital.

When Horatio's nemesis, Walter Resden targets someone close to him, Horatio tries to stop him. Also Eric Delko's relationship with Natalia is tested when she thinks she may be pregnant.

The CSI team must locate a woman who has been kidnapped and dialed a wrong number on her cell phone. To try and find the woman the team must first figure out whom the kidnapped woman was trying to call in the first place. Marisol has a difficult decision to make and Horatio helps her. Natalia is surprised when Ryan asks for Delko's permission to take her out on a date.

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 Mala Noche gang trial is obstructed when the defendant goes free with the help of the witness who is testifying. When a hit ordered by the Mala Noche gang on Horatio finds the people he loves lives are in danger. Delko finds that an ex-lover is disturbing any woman who he is now close to.

In this thrilling season finale, the loss of one of their own is the first hit the lab will take. Getting back to the lab to process the evidence, they find it has been taken over by Federal Agents looking for stolen money from a previous case.