The episode opens with the NCIS team staking out a bar, which they think a suspected thief known as "The Snail" is about to rob.
McGee and Bishop confront the thief - Wayne Levinson - in a back room. He drops a wad of cash on the ground but then tries to make an escape. Tony cuts him off in the parking lot, and Gibbs arrests him.
The next day, Vance calls Gibbs aside and quietly informs him that his father has died of a stroke. Gibbs heads back home to close the shop and to arrange for his father's burial. While there, he meets his father's assistant, a man named Cal Frasier.
Vance calls the rest of the team into MTAC to get briefed about an arson that took place on the U.S.S. Niagara. The fire was set to provide a cover for the attempted escape of several "Brotherhood of Doubt" terrorists who were being interrogated by the CIA. The attempt was only partially successful, as only two of the prisoners were able to get away in a Navy RIB (Rigid-hulled Inflatable Boat).
NCIS tracks the RIB to a place on the coast of Delaware. They discover the body of one of the escapees, plus some DNA samples belonging to the other escapee. Or so they think.
They know that the escapee is a Brotherhood of Doubt terrorist named Lateef Mir, who they later discover paid a visit to the bar that the team had staked out a few nights previously.
This means, the thief was not a thief at all. Under questioning, Levinson admits to collecting the final half of his payment for the provision of two Glocks - which Mir had picked up. The money he had in his hand when confronted by Bishop was his own.
The team tracks all of the activity back to Gibbs' old nemesis and cartel kingpin - Alejandro Rivera. A man whose father Gibbs had killed a few years previously.
It turns out that Rivera had teamed up with the remaining members of the Brotherhood of Doubt, and had bankrolled the escape attempt with the understanding that anyone who made it out would hunt down and kill Gibbs.
Against strict orders from Vance to leave Gibbs alone so he can mourn his father's death, Tony calls him to let him know what's going on.
Gibbs arrives at his home, only to discover that the hot water tank in the basement is leaking badly. As he gets down into the puddle to fix the leak, he notices a hacksaw beneath the water heater. He then notices a live wire that's about to touch the water.
A few moments later, the lights in the house go out, and a man is seen going to the basement to make sure Gibbs was dead. It appears to be the missing terrorist. As soon as he makes an appearance, Gibbs shoots him dead.
When Ducky examines the body, he notices that the man's fingerprints have been burnt off with acid. They figure that's just his modus operandi - as he is known to be a chameleon, able to change his identify and appearance at will.
Gibbs pays a visit to Rivera in prison, to let him know about his utter failure. Rivera is enraged.
Abby discovers that the man they thought was Mir was another assassin entirely. Mir is still out there, hunting Gibbs. They try to call him, but he doesn't pick up.
Gibbs is in his father's garage when he notices someone has come in. At first, he thinks it's Jackson's assistant, but then notices that it's someone else. The man shoots at Gibbs but misses.
As he makes his way around the truck, Gibbs knocks the gun out of his hand, so that it goes beneath the truck. Mir dives for it, and just as he turns over to shoot Gibbs, Gibbs knocks the block out that's holding the truck up. The truck comes down and crushes Mir.
Just before his father's funeral, Gibbs hands over the keys of Jackson's shop to Cal, his assistant and tells him to take over the shop - that it's what his father would have wanted.
After the final scene where Jackson is given a full military funeral, there's a final photo of Mark Harmon and Ralph Waite, arm in arm in front of car. The photo caption reads "In Memory of Ralph Waite. A Gifted Actor and our Friend."