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Before the start of his shift, Keppler eats dinner at a diner where he runs into an older man named Frank McCarty. Frank, who appears to know Keppler from New Jersey, asks Keppler for a favor, but Keppler quickly says no before Frank can explain.

The CSIs are called to a hotel room where a man and a woman have been shot and killed; the woman's left hand has been cut off. Brass informs them the man is Dennis Graves, a cop from Trenton, New Jersey. and that Frank found the bodies. Keppler denies knowing either Graves or McCarty, despite also being from Trenton.

Brass questions McCarty, who says Graves picked up a prostitute that night. Nick finds long blonde hairs and shoe impressions in the bathroom; neither matches either victim. The CSIs realize a witness may have survived.

During the autopsy, Doc Robbins removes butt implants from the dead woman. The serial numbers on the implants lead to Courtney Evans, and Warrick goes to her house to process it. Grissom. who has returned from his sabbatical, joins him at the house and asks Warrick how the lab was during his absence. Warrick tells Grissom about the friction in the lab caused by Keppler's use of reverse forensics. Nick learns Courtney's implants were paid for by a pimp named Ricky.

Keppler meets Frank at a bar. Frank tells Keppler he cut off Courtney's hand because she scratched him; he had to make sure the CSIs could not get his DNA from her nails. He also says he killed Graves because Graves was about to be indicted, and he would have told the grand jury about Frank going vigilante and killing a drug dealer. He thanks Keppler for killing the man who raped his daughter, Amy, but then threatens to expose him as the murderer if Keppler does not clear him of the Graves/Evans murder. Frank tells Keppler he still has the gun with the dead man's blood and Keppler's fingerprints on it. If Keppler were exposed, not only would he be arrested, but every case he ever worked would be tainted and the criminals set free.

Fingerprints at Courtney's house lead to a homeless man, who says he found her purse in a dumpster and went to her house to return it to her. Keppler calls Catherine, who tells him about the dumpster; Keppler says he is nearby and offers to process. At the dumpster, Keppler finds Courtney's missing hand. However, when Catherine asks, Keppler says he found nothing there.

Nick and Archie find elevator video footage of Frank and a blonde. Because Frank had previously denied any knowledge of a blonde woman, Nick begins to suspect Frank is a dirty cop. Nick, Keppler, and Sofia go to Frank's hotel room and find it has been cleaned out. The only thing in the room is a paper bag with a bloody gun in it. Nick is confused, but excited the killer has given them such damning evidence, but Keppler worries the gun is the gun he himself used to kill Amy's rapist and not the one Frank used to kill Graves.

Grissom and Sara reunite at the lab, but Sara backs away from Grissom, saying she has been processing a trash dump site and smells bad.

Archie finds a voice mail from Suzy, the blonde, on Courtney's cell phone. In it, Suzy tells her friend Frank kept calling her Amy. Keppler is stunned to hear this. He leaves the lab. Through flashbacks, he realizes Frank raped Amy and allowed him to kill an innocent man.

Nick runs the fingerprints from the gun and find they lead to Keppler. Nick takes this evidence to Grissom, Catherine, and Warrick. They discuss the possibility of him being set up, but also speculate he may be dirty. Grissom orders his team to treat Keppler like a suspect.

Archie and Greg track Keppler to a deserted field in Henderson using his car's GPS. but Keppler disables it. They begin to track his cell phone.

Brass calls Trenton PD and learns about the history between Frank and Keppler. He calls Catherine to tell her his suspicions that both Frank and Keppler, along with Graves, are dirty. Catherine and Sara learn Suzy works out of a motel called the Blue Siren.

Keppler finds Ricky and demands to know how to find Suzy. He then calls Frank and tells him to meet him at the Blue Siren. Frank comes to the motel and enters a room where Suzy is waiting. Frank points a gun at Suzy, but Keppler enters and points a gun at Frank. Keppler confronts Frank and accuses him of raping his own daughter. Suzy runs out of the room, but when Frank fires at her Keppler takes the bullet. Catherine then bursts into the room, where Frank proceeds to point his gun at her, but Keppler quickly fires at Frank six times, killing him. The police arrive and Keppler is rushed to an ambulance, where he dies. Catherine bursts into tears and is led away by Grissom.

Nick and Warrick head out to the deserted field in Henderson, where they find a cooler with the hand and Keppler's cell phone inside. Keppler had left a note telling the CSIs to check under the nails for Frank's DNA.