The body of retired Lieutenant Commander Runyan Hayes is found in the woods. He'd been shot to death about two days prior.
Ducky recognizes the name. He reveals to Gibbs that he had been investigating a case connected to Hayes, as part of his secret amateur sleuthing club that investigates cold cases.
Ducky tells Gibbs that Commander Hayes had contacted his group three weeks ago for help in a case where his son Michael was convicted and sentenced to life in prison for the murder of Lieutenant Brett Swannie, a murder he says his son never committed. Hayes told him he believed that the real guilty party was Todd Bennett, a fireman. Hayes was going to confront Bennett and get him to confess.
Bishop notes that hairs found on Swannie's body matched Michael Hayes and on that basis he was convicted.
On re-investigating the murder scene, Tony puts his finger into a hole where the bullet that killed Hayes had hit, and comes away with a splinter.
Gibbs and Bishop pay a visit to Ducky's secret detective group. They gather all of the evidence the group has gathered thus far.
Jason and Natalie Tupperman, who are friends of Commander Hayes and his family, agree to be Makaela Hayes' guardians. Jason tells Gibbs that Michael is like a brother to him.
Tony informs Gibbs that the hair test that was used to convict Commander Hayes' son Michael was flawed, discredited. Lyle says that the test is no longer considered part of the legal process. It turns out Abby ran the hair test that was used to convict Michael Hayes. The test was called the "Microscopic Hair Comparison Analysis".
Tony, McGee and Bishop present Gibbs with a silicone impression of the hole left in the tree that once contained a bullet. The impression shows that the bullet was dug out by a key, rather than a knife.
Lyle notes that McGee and Tony had tree sap on their shoes. He tells Gibbs that peanut butter removes tree sap.
Abby tells Gibbs that Michael Hayes DNA does not match the hair that was found on Swannie's body, the man he supposedly killed. This proves he was falsely convicted.
Gibbs asks Abby if she could match the DNA of sap from the tree into which the bullet was fired, to the sawdust found on a key. She tells him she can.
Gibbs digs out the splinter from Tony's finger.
Gibbs asks Jason Tupperman to come into NCIS. Bishop offers him a glass of water and then takes it away once he's done with it. McGee asks him if he found parking okay. Tupperman says he had no problem since he used their valet.
The "valet" comes into the bullpen. It's Palmer, dressed as a valet. He holds up Tupperman's car keys in a baggie.
Tupperman confesses to killing Swannie. He says he wanted to confess after they arrested Michael but says he just couldn't do it. He says he did not regret killing Swannie but does regret letting his best friend take the blame.