We flashback in time to see what really happened before Horatio got a DNA analysis from Maxine Valera saying Horatio's son was involved in something. In the beginning of the flashback, we see S.W.A.T. units and the CSI team closing in on a mystery man's home. But instead of getting caught, the mystery man jumps right off the building roof and in to a boat and manages to escape. Afterwards, Eric continues being jealous of the new relationship between Calleigh and Jake Berkeley and Horatio faces emotional moments with his son.

The Internet turns Candace Walker into a very popular sex symbol, but with bad consequences as her boyfriend is murdered during a swimming competition. With the tragedy, Candace grows as an international sensation, leading to Ryan becoming her private protector. However, things don't work out like they should when the CSI's are exposed to the public, making them fear that the next victim may be one of their own.

What seems to be a normal day of transferring criminals from trial to prison takes a turn for the worst when the prisoners punch down Frank Tripp and the driver and escape. One of the prisoners who escaped was Horatio's son Kyle, who later on goes missing.

A date in a car turns into a death meeting when the car explodes and the girl dies. The boy manages to get out of the car, but is on the edge of losing consciousness when he's found lying partially into a nearby ocean. Meanwhile, Alexx believes she has found something big while autopsying the young girl who died. Also, new evidence is collected and analysed that suggests Tim Speedle may still be alive.

A call from a mysterious woman ends in death for a sport legend and Alexx uncovers something odd about the killing at the crime scene. She also talks to the sport legend's wife, who has a court order that his body will be frozen and no autopsy will be made. However, Alexx takes part in a Virt-opsy (Virtual-autopsy). Meanwhile, Calleigh talks to the mysterious woman, whom they identified with the legend's phone records.

The CSI's investigate a case where a man was strangled to death during a total solar eclipse, but Alexx fears that the body will "take another soul" as there's an old saying that it won't get rest until it has done that. Meanwhile, Natalia gets a DNA result that suggests a person's DNA is mutating into a canine, as in a wolf.

One of the models at a fashion show is killed by electrocution while walking down the runway and Horatio believes the killer was sending a message to them. When Ryan and Calleigh check out the wires below the runway, they uncover that each of the models had their own personalized lighting, and that a small fire made the evidence burn and disappear. Meanwhile, evidence that is found at the scene leads Horatio to a prisoner who, appearently, was the dead model's husband. Horatio also visits his son in prison, who is having a hard time in there.

A seemingly normal family vacation turns deadly when assassination attempts on all of them are made. Only one of them dies, though, and he was in an elevator that appearently was having problems. Natalia is the first one at the scene for the first time and gets an odd feeling that he is trying to tell her something. Meanwhile, the CSI's get their first suspect and the man of the family want to get revenge on him. However, Horatio isn't sure that the suspect did it and must therefore make sure the family man doesn't get an opportunity to kill him.

Calleigh's life is threatened when two unknown gunmen two times try to kill her. She manages to survive and get the car to crash, though, but one of the gunmen escapes while the other dies. At the scene afterwards, Horatio and Ryan find some irregularity in what was inside the car. Meanwhile, Calleigh is being questioned by Stetler about what happened and she gets mad when Stetler believes her memory is affected by drinking alcohol before the incident.

The CSI's investigate the death of a wealthy family's nanny, found by the family daughter whose feet were covered in the nanny's blood. While talking to the son in the family, Calleigh and Delko find out that the nanny was quitting, but they also find some irregularity in her bags. Later on, while searching a suspect's car, the family notices that they have been robbed, leading Horatio to think the nanny "died for the money".

Three weapon smugglers checking their weapons are in for a shock when an unknown man walks silently in to their secret location. The unknown man shoots and kills all of them with a rare but illegal gun that can "vaporize" human. Horatio believes someone is sending a message, and when Maxine Valera uncovers that there was a fourth man with the same job as the victims, Horatio makes him an instant suspect for their deaths.

While investigating a young woman's death in her apartment, Ryan and Alexx try out a new technique for recovering prints off the victim before moving her. However, a fire breaks out in the apartment, which spreads over to the victim. Ryan tries to find a fire extinguisher, but finds a meth lab in the apartment instead. Ryan believes it was his tent (for the technique) that started the fire, but Calleigh, Eric and Natalia find out that the fire was a ticking time-bomb because the electricity in the room wasn't able to turn itself off, leading to a fire.

Julia Winston, Horatio's ex and Kyle's mother, re-appears as a rich widow when Horatio and the team investigate a man's death in his own office. However, Julia's appearance is a case of its own and Horatio and her share some emotional discussions concerning custody of Kyle. Meanwhile, Alexx gets stuck in traffic and Natalia notices that some blood at the crime scene has been touched and "moved".

A murder bride at a wedding finds an unexpected suspect in the groom, a professional baseball player who was standing right next to his bride when she was shot from a distance. The investigators head to the site of the bachelor party, a strip club where one of the strippers was stiffed by a member of the stag party.

Horatio must once again face his past when Julia arrests him and has him extradited to Brazil for a murder two years earlier. Meanwhile, Calleigh's alleged work mistakes are being put on the internet by an unknown cyberstalker.

Horatio is transported back to Miami to help the team find Calleigh, who's been kidnapped and forced to cover up a murder. While at the scene of the kidnapping, they notice that an ambush took place, involving Calleigh fainting from chloroform. Later on, one of the kidnappers turns himself in to the CSI's and tells them the location of Calleigh... but to arrest the remaining kidnapper without Calleigh becoming a victim, they cook up a poker plan, hoping that the kidnapper will "fold" after "all in".

The CSI's investigate the death of an Internet predator that was overdriven while talking on the phone. Alexx uncovers that the victim’s clothes was partially covered in oil, meaning that the car that killed him was leaking. Meanwhile, Delko and Frank Tripp interrogate the woman that the victim was talking to, who apparently had a “fling” with the victim a few months ago. Afterwards, another body is found and Natalia recognizes the killed man from a show called “Predators Among Us”. He had been talking to a girl named Tiffany, which takes an unexpected turn in the case.

When a man crashes down a sinkhole after some road rage, Horatio and Frank uncover a bank vault underground, which leads to the suspicion of a bank robbery. They also find the body of a woman that they believe was in on the robbery but left for dead when the car came crashing down. Delko talks to the bank manager, who denies that anyone can break in to the vault, especially the woman. Meanwhile, the team gets suspicions that the workers who transport oranges from factories to stores hide cocaine in special compartments inside the crates.

Alexx must decide between professional duty and family duty when her son becomes a suspect in a murder case. As the investigation goes on, Alexx finds that saving her son may have dire consequences.

When a fake 911 call causes a man (holding a knife) to die, Horatio uncovers something odd about the crime going on. Meanwhile, Calleigh talks to a suspect whose house was identified as the caller's location, but he denies that it was him. Later, Horatio argues with a private investigator who is determined to destroy the CSI team.

In the season finale, the CSI’s investigate the death of a man who fell backwards out of a window and on to a street. However, an unknown individual doesn’t want the team near the victim and starts a gunshot battle, ending in one more fatality. Afterwards, the lives of two team members are threatened and a bullet has Horatio Caine's name on it...