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.

Evidence leads the CSIs to believe that someone started a massive fire in the Everglades in order to cover up a murder. Local prisoners are brought in as free manpower to help fight the wild fire in the Everglades. However, when a serial killer escapes the scene, Horatio must track him down before he strikes again. Meanwhile, the body of a local college student is found shot to death and the fire has destroyed the crime scene and the evidence. However, when the team uncovers an illegal moonshine operation and homemade ammunitions in the vicinity, the CSIs uncover the real reason why the boy was out there.

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.

While investigating the murder of man hired to make dirty bombs that terrorists intend to set off in Miami, Horatio finds the bloody fingerprint of his brother, Raymond, who he believed to be dead. However, when Raymond's son is kidnapped, he emerges from deep undercover and the estranged brothers must work together to save the boy. Meanwhile, while processing a crime scene, an unknown assailant holds a gun to Calleigh's head and, after a deadly confrontation in her gun lab, she is left doubting that she can continue as a CSI.