When the body of Lt. Commander Runyon Hayes is found in a wooded area, Ducky recuses himself from the case, calling in another medical examiner to perform the autopsy.
He tells Gibbs, "I know far more about this man's murder than I care to admit. Talk to Todd Bennett, a fireman in Wolf Trap, Virginia."
When pushed, Ducky admits that after failing at online and speed dating, he tried mental stimulation by joining the Sherlock Consortium for Investigation, which solves cold cases. Three weeks ago, Hayes reached out to them, desperate because his son Michael is serving a life sentence for a military murder he says he didn't commit. The commander thought Todd Bennett was the real killer.
Gibbs and Bishop go to see Bennett, who tells them that he knows Runyon Hayes thinks he committed murder and he saw Hayes a couple of weeks ago. But Bennett says he isn't a murderer. When asked how he knew Hayes was dead, Bennett hands them a card from Judith McKnight, a private investigator who happens to be a member of the Sherlocks.
Gibbs forces Ducky to take him to a Sherlocks meeting. Ducky is reluctant because the group doesn't play well with others. Gibbs says neither does he.
Gibbs and Bishop meet with a trio of Sherlocks: Judith, ex-cop Walt Osorio and Lyle. Ducky tells the Sherlocks that NCIS is taking over the investigation of Runyon Hayes's death and he asks them to hand over any information, explaining his loyalties lie with NCIS. Judith flirts with Gibbs, commenting that he has big hands. When the Sherlocks don't cooperate, Gibbs brings them into NCIS for questioning.
McGee is excited to meet Judith, a fellow author who writes mysteries featuring a 14-year-old crime-fighting female with pigtails. He just happens to have a copy of one of her books in his desk.
While DiNozzo, Bishop and McGee question the Sherlocks, Gibbs meets with Runyon's granddaughter and her new guardians. One of the guardians, Jason Tupperman, tells Gibbs he wants to be the one to tell Michael about his father's death. "We were close like brothers," he says. "We served together. I still visit him. He's one of the best men I know. He's innocent."
McGee calls Gibbs and has him come back to NCIS as the Sherlocks have discovered something. The forensic hair test used to link Michael to the murder in 1999 was flawed and has since been discredited. The forensic scientist who performed the tests was Abby.
Abby says she has sent her flawed cases to the FBI already. But now she is worried that innocent people went to jail because of her.
Jason and Bishop go to see Michael to tell him about his father's death. Michael doesn't want to have anything to do with Bishop because she is NCIS, saying "I haven't held my daughter's hand in 16 years. Can NCIS help me do that?"
DiNozzo and McGee, who went back to the forest when it was ascertained that Runyon Hayes was murdered, produce a silicon impression of the three where the bullet had been lodged. But it looks as if someone dug it out with a key.
Meanwhile, Gibbs is at home with an ice pack on his knee. The Sherlocks stop by – Walt sleuthed out Gibbs' address. Walt tries to convince Gibbs to work with them in the name of justice. But Judith is more interested in getting Gibbs out of his pants. She flirts outrageously, asking him if the basement is his naughty room. Gibbs turns down the Sherlocks' help -- and Judith's offer.
The investigators need Michael's DNA. Abby pleads with Gibbs to get a sample for her because she's responsible for putting him in jail. She asks Gibbs to fix this because fixing things is what he does.
When Bishop and DiNozzo get to the prison, they are told Michael's parents are there. But, of course, his parents are dead. They mystery couple turn out to be Judith and Walt.
Back at NCIS, Ducky takes the Sherlocks to task over their illegal, meddling ways. Lyle makes an off-the-cuff remark that peanut butter removes tree sap from leather. He explains he said it because DiNozzo and McGee had stains on their shoes from their trip to the woods.
Gibbs jumps up, saying, "You just solved the murder." He asks Abby if she could match a sawdust sample to a tree. She says, of course, trees have DNA.
They invite Jason Tupperman to NCIS. Bishop gives him a glass of water to get his DNA, and Jimmy Palmer pretends to be a valet to get his keys. The keys have wood on them from the same tree that DiNozzo and McGee took the silicone impression. They just happen to have a sample of it because DiNozzo has a splinter from the tree in his finger.
Ducky plays Jason's taped confession for the Sherlocks, and then resigns. Judith tells him that she will see him. She and McGee are collaborating on a new crime novel and she is basing her main character on Gibbs, the silver-haired devil: "Short on words but his eyes say plenty."
Ducky names his replacement: Jimmy Palmer, who comes in wearing an itchy Sherlock cap.
Michael Hayes is freed and hugs his daughter for the first time in 16 years. He thanks Gibbs and Abby. Abby tells him, "I put you in here." To which he responds, "No, you're the one who got me out."