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A man dressed as a clown walked into a bakery and shot the owner. Police dealt with some confusion as the suspect was fleeing the scene and an army of look-a-like clowns appeared on the street. The clowns were all held as possible suspects, one clown told Flack that there was an ad on a website promising money to people showing up at that street corner if they were dressed as a clown.
A clown suit was found tossed into a dumpster near the crime scene, and odd trace off the suit and the body of the murdered man caused some confusion. The CSI went to the local clown registry and received the name of the man who was specially registered to the exact clown face witnesses saw at the bakery. Flack and Danny found the man tied up and slightly beaten, and after processing the man's apartment the CSI uncovered a finger print.
The finger print belonged to Bobby Renton, a man who seemed to have vanished five years early. Jo surmised that since Bobby appeared to have disappeared all in one day that he might be in the witness protection program. She was right and her ex-husband paid the office a visit to see what the N.Y.P.D. wanted with someone under protection. He also revealed that protection for the witness had been requested by Flack.
Bobby Renton had been placed in the witness protection program after testifying against drug dealers. He was sent to Memphis, and not coincidentally the body of a hit man was found shot to death there. The bullets used in the hit man's murder matched the bullet fragments found in man shot at the bakery. The CSI pieced together that the man shot at the bakery had been the godfather of one of the men Bobby Renton had helped put in jail.
Bobby was not satisfied with just killing the man who had put the hit out on him. He lured Flack out to where he was hiding and was going to kill Flack as well for talking him into joining the witness protection program, because it had cost him a life with his girlfriend and son. Flack managed to convince Bobby not to shoot and eventually apprehended and arrested him.