Při instalaci nového kotle v jedné škole vypadne z komína vyuzené lidské tělo. NCIS prochází seznamy pohřešovaných osob a všichni jsou zaskočeni špatným odhadem doby úmrtí, kterou stanovil Ducky. Své původní tvrzení šest měsíců totiž změnil na 5 až 6 let. Při snaze identifikovat mrtvého naráží NCIS na problém - FBI zablokovala k údajům přístup. Jde o sériového vraha, který má na kontě přinejmenším 14 vražd dívek a žen a po kterém FBI pátrá přinejmenším 12 let. NCIS se ale případu nehodlá vzdát.

Nalezený muž je identifikován jako Charles Bright a detektivové se vydávají za jeho ženou Karen a jejími dětmi. Byla to právě ona, kdo nahlásila muže za pohřešovaného a přesvědčuje vyšetřovatele, jak milující manžel to byl a že se mu coby stavebnímu inspektorovi musela stát nehoda. Na dvoře jejich domu se však najdou pozůstatky dalších obětí, podobně jako ty předchozí všechny svým vzhledem připomínají Karen a chybějí jim dva prsty u nohy, právě tak jako jí.

Mezitím má tým nemalé problémy s "fiktivní" knihou DEEP SIX, kterou McGee napsal o agentech NCIS. Rozhodně z ní nejsou nadšeni...

While replacing a furnace at a Quantico Marine Military Base middle school, workmen removing the old flue has something fall out when they get it loose. "More than just carbon here." They discover the well-preserved body of a man.

Ziva and Tony are seen sitting at their desks reading "Deep Six'" and talking about various parts of it. They go to the garage and are met by Tim at the van. Ziva states that she is driving and Tony calls shotgun. They don't even allow McGee to sit in the front. We see McGee peering through the communication window and begging to be allowed to sit up front. Ziva peels out of the garage as we see Tim fall backward while hollering "It's only a book!" The team arrives at the school and quickly determines that the dead man is not military personnel and when Gibbs asks NCIS Medical Examiner Dr. Ducky Mallard the time of death (TOD) he is greeted by the doctor tersely, further indicating Ducky’s apparent resentment of Gibbs' “quitting” NCIS. Ziva and Tony confront Ducky on his hostile behavior toward Gibbs. Ducky blows them off and estimates the TOD as two to four months previously.

Using Ducky’s TOD, the team scour missing persons’ reports from the period and finds no one meeting the deceased’s description whom they call "Crisp Kringle". Ziva and Tony have a close encounter, in which Ziva says "It takes all of my willpower to resist the urges you stir up in me when I'm around you." Tony replies "I thought I was getting that vibe from you when we went undercover." "Yes I wanted to do it the first night!" "Oh yeah," Tony half moans. "But my father wouldn't approve." "Because I'm not Jewish?" "No, because he doesn't like it when I KILL my coworkers!" exclaims Ziva. Gibbs comes in and breaks up the encounter and wants an ID. Tony admits he has none at the same time that Ducky enters and owns the responsibility because of a faulty TOD. As it turns out, the deceased did not die two to four months earlier, but "five to six.." Tony interrupts "five to six months might work." Ducky admonishes him with "Not months, Tony, YEARS." Ducky reasons this is because the body was preserved by the smoke generated by the furnace.

The scene shifts to McGee and Abby in the lab where Abby gets a hit on the corpse’s fingerprints, but is surprised when the AFIS system denies them access and starts deleting the files. The scene abruptly changes to the MTAC where Jenny orchestrates the surveillance of some foreign operatives leaving a small private jet and entering the USA at an airport. She has Tony mark the bags with GPS devices, without the knowledge or permission of Gibbs. They get some photos through a small camera that Tony is wearing and get some pictures of the people from the plane.

Back in the lab, Abby tells Gibbs their mystery hacker was the FBI and they deleted the fingerprint files. Gibbs already knows because his old friend and nemesis FBI Special Agent Tobias Fornell has arrived to pick up what he claims to be his body. at the same time that Ducky and NCIS Medical Examiner Assistant Jimmy Palmer discover a human toe in the stomach of the corpse.

Fornell identifies the corpse as a cannibal serial killer that the Agency has been tracking for the over a decade. The murderer’s trademark was gnawing off the toes from the left feet of his victims. The Agency does not know the corpse’s age but did find the prints at a crime scene. Gibbs and Fornell bump heads and Gibbs remains in control, taking Fornell to show what the corpse looked like in life, identified at Charles Bright, who disappeared five years and seven months ago. The team gets an address, and after obtaining a search warrant, delivered by the NCIS legal eagle Special Agent Michelle Lee, they all head there.

Gibbs and Fornell go to question Bright’s wife, Amy Bright, who has two children. Fornell freaks out when he sees Amy Bright, who looks like all of the alleged murderer’s victims. Meanwhile, Tony finds "bone fragments" which turn out to be a skeleton in the Bright’s backyard. Bright was identified as a building inspector for the Department of Defense and was scheduled to visit the middle school where his corpse was found when he disappeared. Gibbs does not believe that Bright’s death was an accident. In the back yard McGee asks "Why are we letting the FBI do the digging?" and gets the reply "We're letting them do our manual work." The FBI uncovers several more skeletons. Ducky declines to offer a TOD on bare skeletons and proceeds to tell a story of how he, Gibbs, and Jenny had a French warrant for their arrest after Ducky pushed a French officer off a 60 foot cliff -"With a lake at the bottom!" "Gibbs and I had to escape on a small sailboat." They were fugitives until a fairly new, young agent persuaded them {the French authorities] to drop the charges. "Jenny, uh, Director Shepherd?" "She was the one who procured the boat." Ducky recalls this fondly and the thaw with Gibbs begins.

Gibbs and Fornell return to question Amy Bright, who vehemently denies that her husband could have been the murderer in spite of the fact the authorities were removing four bodies from her backyard. The tearful Bright is convincing. Mrs. Bright asks Gibbs "You ever have a feeling that something terrible happened?" "Once" Gibbs replies. Perhaps the murderer was not her husband.

At headquarters, Ducky and Gibbs have a heart to heart about Ducky’s animosity toward Gibbs. Ducky says that "since your return I've been acting like..." "An ass?" Gibbs replies. Ducky explains his feelings were hurt that Jethro did not tell him goodbye when he quit even though Ducky had given Gibbs a ride home nor about his murdered family. Gibbs stands up from behind his desk and comes around face to face with Ducky. "You know how I feel about apologies, Ducky." "It's a sign of weakness." "Not between friends. I'm sorry Ducky." "There is something I should have said months ago." Ducky puts out his hand and says "Welcome home." Gibbs hugs him and whispers "Thanks" in Ducky's ear. The rift is completely resolved.

After Tony and his paramour finally do the deal, the scene shifts to the next morning and Ziva detecting that Tony had enjoyed sensual release the previous night. Fornell enters with a Justice Department Order to turn the body and investigation over to the FBI immediately. While Gibbs, Fornell, and Jenny discuss the situation in the Director’s office, Ducky calls Gibbs and announces that he has determined the cause of death of the smoked corpse. Gibbs says to Fornell "Come look at something" and Fornell replies "You've got that moustache in a box don't you?" In Autopsy Ducky points out to Fornell on a CT scan of the body several abdominal punctures done with either an ice pick or a Phillips-head screwdriver. He had initially missed it due to the shrinkage of the tissues from the "smoking." The man was murdered on a marine base saving the case for NCIS’ attention. Fornell grips to Gibbs "You're enjoying this aren't you?" to which Gibbs comes back with "Only slightly more than a lot!"

Gibbs dispatches everyone to find out who wanted Charles Bright dead. Ducky tells Fornell and Gibbs that the bodies recovered from the Bright house had no definable TOD. Ducky evaluated the profile of the killer and discovered that he more than likely knew his killer, hence the ultimate identification of his wife. This leads to connections Bright would have had at the middle school where he was working and this ultimately points to Amy Bright, who worked there as a part-time teacher before she married Bright. And was substituting the day of his disappearance.

Abby goes to see Marty, who is a forensic botanist, to evaluate the growth of a bush's roots through the skeletal remains found in the Bright’s backyard. Amy Bright is brought in for questioning and gives up that she discovered her husband was a killer and killed him to protect her family. Amy Bright reveals toes missing from her left foot, further sealing the deal against Charles Bright. Right when Fornell was about to let her off the hook, Abby interrupts Gibbs’ interrogation to give him the news that Marty had determined that the bodies in the Bright’s backyard had been buried more recently than five years ago, Gibbs identifies Amy Bright as the serial killer but leaves us with the question, “What is a toe doing in her husband’s stomach?”