The season finale of NCIS begins with Tim at the Green Star Bar and Grill getting some drinks. As he is walking away, a woman bumps into him, purposely flirting with him. However, Tim informs her he is at the bar with someone, and he walks over to a table where Ellie is waiting for him. They are talking to Tony and Gibbs through headpieces, and the two men are in a surveillance van watching the bar. They are looking for a burglar named Wayne “The Snail” Levinson. Soon, Tim spots Levinson enter the bar and after waiting a few minutes while he goes into the back room, Tim and Ellie go to search for him. After finding him holding cash in his hands, Levinson leads Tim and Ellie on a chase through the street, ending with Gibbs and Tony stopping him with their car. As they are arresting him, Gibbs gets a flashback of himself with his father.
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In the squad room on the television monitor, there is a news story on about a fire on the U.S.S. Niagara. Meanwhile, the team talks about the arrest of Levinson, including how the bar owner was going to change the name of the bar to The Lucky Star, since the team was there to stop Levinson. As they are talking, Vance shows up on the stairs and calls down to Gibbs. Upon going into Vance’s office, Gibbs at first thinks he is there to discuss the Levinson case. But Vance has sad news for Gibbs. His father passed away from a stroke.
After the credits, we see the team in the squad room as Abby is looking through photos of flowers to send to Gibbs. She desperately wants to do something for Gibbs and she is afraid to stop stressing over the flowers or she will be sad. As Ellie had never met Jackson Gibbs, she asks them to tell her what he was like. Abby comments on his nice hugs, Tim mentions him giving Gibbs “The Gibbs stare,” and Tony brings up the sweater Jackson had given him in a season six episode. They figure the best thing to do for the boss is to work the case, which Vance agrees on as he asks Tony, Ellie and Tim to come to MTAC.
They find out through a videoconference with Sandra Jenkins of the CIA and Captain Arnold Craig that the fire on the ship was actually intentional and it was carrying prisoners, mainly terrorists. Two of the prisoners escaped and there is thought that some of the prisoners may have been linked to Benham Parsa’s Brotherhood of Doubt. It is believed the escapees were able to use a Rigid-hulled inflatable boat for escape. Tony leaves MTAC to give Gibbs a call, but Vance orders him not to call Gibbs, and to give him time. Tony is confused, as he knows Gibbs would want to be in on the case, but he finally relents.
Meanwhile, Gibbs walks into his father’s store in Stillwater and he is silent as he walks through the building. He finds his father’s cane and sees his Winchester on the wall where it has always been. He has a memory of his father saying that despite telling his son not to touch weapons, he grew up to be a sniper.
Back at the squad room, the team is going over the case and how the prisoners escaped. They figure they escaped through the use of the RIB during the confusion of the fire. The two escapees names are Edwin Smith and Lateef Mir. Mir is linked to Benham Parsa whereas the former is not. Tim tells them Mir is able to change his appearance very easily, so finding him will be difficult. Abby rushes up to them, having sent an e-mail to Tim of a satellite image. The image shows an object matching the description of the boat at a state park in Denver. Tony and Ellie go to the beach, where they spot the boat and the dead body of Edwin Smith.
Ducky and Palmer soon arrive at the beach to examine the body, first to take time discussing Breena’s pregnancy and the possibility of future adoptions. They examine Smith’s body and deduce that he had been strangled. He was good at boat navigation, so once he wasn’t needed anymore Mir killed him. While investigating, Tony receives a call from Gibbs. He ignores the call, something that shocks the team since they never ignore a call from Gibbs.
Gibbs goes into the garage to look around after leaves a message for Tony. He finds a box and brings it down, where he then gets a flashback of his parents fighting and his dad teaching him how to work with a nail and a hammer. He his broken from his thoughts as a young man walks in. His name is Cal and he was the employee who had tried to call Gibbs at work. He was with Jackson when he died and he felt bad for not being able to do enough. Gibbs reassures him there wasn’t anything he could do. Cal tells Gibbs that Jackson had saved him from going down a troubled path, and he is grateful to him. Gibbs asks Cal to help him get the store ready to be sold.
Tony and the team are in MTAC discussing the case over videoconference again. They are told Parsa’s second in command, Fu’ad Hansur took responsibility for the fire breakout, but they don’t buy it since he doesn’t have the funding. The team soon is in Abby’s lab, where she was able to match hair found on the boat to Lateef Mir. It also appears that enough hair was found, showing he had shaved his face and head, and bleached his eyebrows so he would look different in appearance. Abby made a new composite based on the changes and added it to their BOLO. She discovered he was seen at the same bar where they had done the stakeout the night before.
Tony interviews Levinson, who denies knowing Mir. He had been hired to exchange three unregistered glocks for money, which was the payment he was removing from the safe at the bar. Levinson had received part of the payment from a woman with a young child. He was hired by a man in prison named Alejandro Rivera, who was part of the Mexican Drug Cartel that had gone after Gibbs years earlier for revenge. Gibbs had murdered Rivera’s father after the man had killed his wife and young daughter.
Meanwhile, not knowing what has been going on, Gibbs is hard at work in the store with Cal. He takes the rifle down and takes out bullets that Cal didn’t know were there. As Cal takes the rifle and some other items to the garage, Gibbs receives a phone call from Tony, who admits things have gotten “worse.”
Tony goes to prison to talk to Rivera, who talks about his sister’s funeral. Rivera claims not to know Lateef Mir. He claims not to have had contact with Levinson over dropping off guns for Mir. As Tony is about to leave, Rivera inquires about Gibbs. When he brings up the murder of his father, Tony claims to know nothing.
Tony and Tim are discussing what has been going on with the case. They find out the bar manager is Rivera’s second cousin, and he claims to have no knowledge of what happened. However, they deduce that the cousin took the guns from the safe while they were chasing Levinson and gave them to Mir the next day. After doing some digging over the prison logs, Ellie finds out the woman who Levinson spoke to is Leticia Gomez, who has an eight-month-old daughter. In the middle of their discussion, Tim sees Gibbs come in.
Gibbs goes up to Vance’s office, upset that his team was in the field without his knowledge. He wants to go back to work, but Vance insists he take time off, like he had done after his wife was killed. Gibbs says it’s different, but Vance won’t back down. Gibbs tells Vance the job is all he has, and to never let his team keep quiet from him again.
Ellie and Tim talk to Leticia, who is reluctant to tell them much. She does admit to receiving payment from Levinson. She admits she and Rivera love each other. However, after coaxing and reminding her that her child needs her more than Rivera, she admits Rivera had made the Reynosa Drug Cartel stronger through connections with the Mexican government. He was funding the prison break through Cartel money. He organized the prison break so whoever escaped would kill Gibbs.
Gibbs is at home when he hears water running. He goes to the basement, which is filling with water due to a busted water tank. When he gets on the floor to fix it, he discovers it has been tampered with. Across the way, he notices water coming close to the electrical wiring, which has been cut. A man enters the basement and before he can go down the stairs, Gibbs shoots him and the man falls to his death, before being electrocuted in the water.
The team is in the basement documenting the body and Ducky asks Gibbs to stop making this type of visit a routine, most likely a reference to the season three shooting of Ari Haswari, who had shot and killed Special Agent Kate Todd. Examining the body reveals the man had acid burns on his fingers to get rid of identifying features. During this exchange, Gibbs has another flashback of his dad. Ducky tells him to go back to Stillwater, but Gibbs has something to do.
Gibbs and Tim go to see Rivera, who believes they don’t have anything to tie him to the prison break. After they reveal Gomez gave him up, Gibbs tells Rivera they were able to find Fu’ad Hansur’s compound thanks to Rivera’s funding and all members of the Brotherhood were killed. Rivera points out that despite the reason Gibbs shot his father, he still was angry with him for taking him away. He believes he has freed the “Devil’s men” and they will get him. Gibbs retorts only Mir escaped and he shows Rivera the picture of Mir’s dead body. Rivera angrily asks the guard to take him back.
The team is talking in the squad room, and Tim is telling Tony about sending a birthday present to Delilah when Abby rushes up to them. She reveals DNA testing done on the body showed he was not Mir, but someone else named Dar Tareen. He had apparently been set up as a hired mercenary to take Mir’s identity. Gibbs is still in danger and when Tim calls him, he is unable to reach him.
Gibbs is working on an old car and can’t hear his phone vibrating. He hears someone come in and assumes it is Cal. When he gets no response from the person, he glances over to see Mir’s reflection in the mirror. While stunned, Gibbs is able to escape gunfire and a fight ensues, in which he somehow gets the gun away from Mir. When Mir gets under the car to retrieve the gun, Gibbs uses the rifle to knock the car down on top of Mir’s body.
Later, on the day of the funeral, Gibbs is in the store when Cal comes in. He gives Cal the key to his father’s store to run it. Cal is nervous, as he has never done something like this before, but Gibbs tells him to just “do good work.” They leave to go to Jackson’s funeral.
The mood is somber as Gibbs friends and team come to pay their respects. Gibbs shares a hug with Abby and exchanges words with L.J. Moore, a friend of Jackson and Gibbs’ namesake. L.J. tells Gibbs his father was proud of him, and Gibbs counters he was proud of his father. As “Taps” is played on the horn, the American Flag draping the casket is folded up and given to Gibbs, who struggles to keep his composure.
Later, Gibbs is looking at the box from earlier, which is labeled Chickadee. He gets a flashback of giving his mom a boat, which is inscribed Chickadee. His mother tells him that his grandfather said that anyone named after a boat will live on forever. The scene ends with Gibbs placing the boat in front of a piece of paper so he can begin sketching it, most likely to build a life sized boat. Before the commercial begins, a photo appears of Ralph Waite and Mark Harmon with the inscription ‘In Memory of Ralph Waite. A Gifted Actor and our Friend.’