Grissom and Sara may be secret lovers, but they still find ways to surprise each other like when their religious beliefs surface when two nuns find a body of a woman crucified on a makeshift cross. The woman was found in a church where the priest may be a man of sin instead of a man of God.

Grissom attempts to get a confession from a neighborhood pedophile by having him help in locating two missing boys. The sex offender is the main suspect. The investigation is more complex than the team ever thought it would be.

The team has a hard time trying to understand Michael who has become a team member since Grissom’s teaching hiatus. They investigate the murder of an unidentified girl who may have been killed by a serial killer who has been killing since the early 1970’s.

At Keppler's request Catherine uses a different approach to catch the killer, and in doing so she deceives the rest of the CSI team. The team soon discovers that something is amiss in Catherine’s investigation.

Grissom returns from his sabbatical; Keppler is put into a compromising position when the bodies of a Trenton police officer and a hooker are found in a hotel room. The man who found them is a retired New Jersey cop and close friend to Keppler, who doesn't reveal their relationship.

When a has-been boxer is killed, the CSIs must establish which of several life-threatening acts actually killed him.

As the CSI's continue their search for and discover the identity of the "Miniature Killer", Grissom and Sara's relationship gets exposed to the rest of the team as she goes missing during the investigation. The "Miniature Killer" is finally captured, but not before a member of CSI becomes the killer's final victim.