The episode opens with a little boy heading for the carousel in a fun park, his father trailing behind with balloon, backpack and fairy floss (sugar candy). The boy asserts that balloons are for babies but that his Dad should mind the other things during his ride. When on the carousel, he keeps looking at his father so he sees two suited men approach his father and take his father away. When the carousel stops, he races over to where his father was standing, but only the fairy floss and backpack are left behind. Our view is from above, and the red balloon floats into the lens of the camera. CREDITS ROLL
In the squad room, Gibbs gives the alert for the team to move, because a Navy Commander is missing. Ziva questions the speedy response and is told that the 6 year old son of the commander called NCIS and is waiting, alone, in the fun park.
DiNozzo gets to the boy first and begins to reassure him, making statements to the boy. He gets no response. Gibbs arrives and DiNozzo tells Gibbs that the boy is in shock. Indignant, the boy replies No I'm not and points out that he was waiting for DiNozzo to actually ask a question. Gibbs supresses a smile, sits beside the kid and asks what questions was he waiting for. The child points out that what did you see? would be a good start. The child gives a comprehensive description, from a child point of view, including noting that the baddies were wearing Ipod earphones but only in one ear. Gibbs and Tony confer, as it sounds like feds but Gibbs points out that not even the CIA would leave a child alone in a park. McGee arrives and reports to Gibbs on getting security tapes. Gibbs tells him to contact the child's mother. Transpires that she died in a car accident. Gibbs says then next of kin. McGee reports that there is no one else. They take the child to NCIS HQ.
At the squad room, Gibbs gets reports. The missing man was working on a secret project, details not given over unsecured line. Ziva brings in the picture done by sketch artist, noting that the child has remarkable powers of observation. She tells Gibbs that social security have arrived for the child: Gibbs tells her the difference between social services and social security. Gibbs goes to the child, Zach, to tell him that he has to go. The child has already spotted the social workers and guessed who they are and why they are there. Zach points out that he can look after himself, and Gibbs smilingly says that he doesnt doubt that (and clearly doesnt. This is a smart and unsentimental kid). Gibbs cajoles Zach into going with the social workers but kneels to give Zach a business card, telling him to call Gibbs at any time.
The team visit the commander's place of work which is in chaos, with power failures and a computer hacking crisis. Their top secret project, Honour which is about encryption and computer security, has been hacked. The harried bosses reassure the team that there is no problem as the last line of defence is that the Commander has the code keys memorised. The team break the news that the Commander is missing, presumed kidnapped.
Tony phones the news to Gibbs, who is in his car on his way to drop off Zach's Ipod to social services, because he had left it on Gibbs' desk. Gibbs then gets a second phone call, this time from Zach. Gibbs assumes that the child is phoning about the Ipod but Zach urgently tells him that the villains are outside social services and that Gibbs must come quick because these men know where his father is. Gibbs tells Zach to wait but Zach yells that they are getting away and races after them. By the time Gibbs gets there, they are about to nab Zach and kidnap him, but the child delivers an elbow to a vulnerable spot on his kidnapper and scuttles away to Gibbs, who starts shooting at the villains' car, shattering the back window.
Gibbs takes the child back to NCIS HQ and puts him in protective custody. Jen manages to keep control of the case with NCIS, although every federal agency wants to claim it as the Honour project breach of security threatens the security of all computer networks in all agencies. The security on the project is so tight that it is assumed it must be an inside job, and the papertrail starts to show that the Commander moved his assets prior to his kidnap.
The team start to confront the question as to whether the commander disappeared by prior arrangement and is a traitor, or whether he truly was kidnapped under threat of harm to his child (hence his willingness to leave with the villains). Gibbs' gut says that the Commander must be innocent and a victim. He points out to Jen that all you have to do is look at the son.
The main interest is the relationship between Gibbs and Zach, which is instantly strong. Zach so resembles Gibbs in manner, reserve, cold logic and disdain for childish behaviour that everyone notices, including Gibbs. Abby says to Gibbs that Zach is a mini-Gibbs, to which Gibbs responds by saying are you calling him a mini-me?, astounding Abby with his pop culture reference to Austin Powers films.
Tony, fondly imagining that he is good with kids, proceeds to patronise Zach who suffers it with patient disdain. Ziva finds this hilarious. Zach manages to remember enough of the villains' number plate for the team to be able to track down the vehicle. When they raid it in a parking lot, they discover one of the villains dead inside, executed by the other villain after having been injured in the shootout with Gibbs earlier.
The staff take turns looking after Zach, but it is Gibbs who takes him home, and shows him how to work on the boat. Zach asks the question as to how Gibbs will get the boat out of the basement. Gibbs says he has never really thought about it, but he could tear down a wall and build a ramp. Zach is reluctant to work on the boat because he doesnt want to get it wrong, so Gibbs gets behind him and guides his hands as to how to see the grain in the wood and work with the grain. Gibbs exhibits the same patience that he always shows to Abby.
Jen visits to try to persuade Gibbs to recognise that the prime suspect in the Honour code breach is, in fact, the commander. Zach, having been sent upstairs to get a soda so that Jen could talk to Gibbs privately in the basement, has crept back to the top of the stairs and listened in. When Jen denounces his father, Zach emphatically speaks up for his dad, tearfully declaring that he knows that his father is innocent. Gibbs points out to Zach that there is evidence against his father, but Zach says he knows his father is innocent because he can feel it in his stomach. Gibbs knows better than to dispute gut feeling.
Back at HQ, Ziva eventually gets some intel from her Mossad connections that reveal that the villains were mercenaries in Bosnia who specialised in torture and that the commander has been kidnapped and framed. Therefore, they assume that the Commander is being tortured for his code key. The race is on to find him after Ziva educates McGee about how no one can withstand true torture-based interrogation, and says how she can get information from suspects in a matter of mere hours.
Abby and McGee and DiNozzo collectively have a breakthrough when a secretary (who caught Tony's eye) from project Honour is spotted on CCTV as having purchased phones used in the kidnap arrangements. Ziva, McGee and Gibbs go to her workplace where she is interrogated with a view to speed of finding the Commander. This means that Gibbs takes McGee out for coffee and lets Ziva question the woman alone. When McGee asks Gibbs what Ziva is doing, Gibbs' look tells McGee that, really, he doesnt want to know. The woman, who had been defiant, is a nervous wreck by the time Gibbs and McGee return from coffee, pleading not to be killed. Gibbs is sanguine about this, whilst McGee looks disturbed. Like the viewer, they are wondering just what Ziva did to get such a result so fast. The woman gives the location of the torture chamber and the team arrive there in the nick of time, killing a villain (who inexplicably started shooting through a closed door, indicating his position, and then opened the door, giving a perfect shot to Gibbs, the sniper). The injured, exhausted commander says he has revealed the secrets, because the villains had brought him proof that they had his son. The proof was the Ipod, which is now in the torture chamber. Gibbs realises that the only person who could have obtained it is the best friend of the Commander, who had visited Zach at NCIS HQ, giving Zach a game player to distract him from the Ipod. Next scene, they nab the best friend who is a traitor on all levels.
Finale is Zach and Gibbs, standing side by side looking out the big window in the NCIS squad room, with Gibbs drinking coffee from big cup, and Zach drinking milk, both passing time. Zach is downhearted that he was duped by his father's friend and ponders how he could have let the friend deceive him. Gibbs kneels, wipes away Zach's milk moustache and points out that sometimes bad people can be very convincing. When asked whether he has ever been duped, Gibbs replies ruefully that it has happened more than once. Zach declares that when he grows up he will get the people who did this to his father and Gibbs gives a wry grin and says that he believes Zach will. At this point, Zach's dad arrives and the serious 6 year old suddenly becomes a jubilant little kid and flies into his (injured) father's arms, declaring that he knew his Dad would come back and saying I love you, Daddy. Gibbs is left, alone, watching from the sidelines and we see a flashback of him working on the boat with Zach and then another, older flashback of a younger Gibbs working on the boat with a little girl.