Jeanne seznámí Tonyho se svým otec, kterým je LaGrenouli. Když společně vyrazí na snídani, Tonyho auto, které řídí LaGrenouliho řidič, nečekaně exploduje. Vzápětí se LaGrenouli i dcera Jeanne ztrácejí z radaru. Do kanceláře NCIS vtrhne rozzuřený agent CIA Kort a chce vědět, kde je Grenoulli. Ukáže se, že známý obchodník se zbraněmi funguje jako informátor CIA a ti ho výměnou za to nechávají být. Ale informace o jeho spolupráci prosákne do podsvětí a LaGrenouliho nepřátelé chtějí zabít jeho dceru. Proto LaGrenouli požádá ředitelku Shepardovou o spolupráci. Ta ale odmítá, protože je přesvědčená, že je LaGrenouli přímo odpovědný za smrt jejího otce. Když jde tým zatknout LaGrenouliho na jeho loï, nevědí, že jeho mrtvé tělo plave kousek dál v řece...

The season premiere starts where season 4 left off: The intro before the credits is a fast summary of the whole Le Grenouille story arc, which ends where season 4 ended...with Tony meeting the father of his girlfriend Jeanne, in daddy's limo. "So nice to meet you at last...Professor DiNardo." Pained smile from Tony.

The opening credits roll and then we are in the middle of Director Shepard's nightmare, literally. She is asleep in her study and we see her dreaming of her father's death. She wakes and the scene jumps back to that limo, where Jeanne's father is being charming and Tony feels most uncomfortable. Does La Grenouille know who Tony is, even though the Frog is referring to Tony as Professor DiNardo? They decide to go for breakfast and Jeanne starts to tell the story of the night's adventures with the druggies at the hospital, when her beeper informs her that she forgot to sign a death certificate. Back to the hospital.

Cut to Ziva arriving at NCIS HQ where she bumps into McGee. "What are you doing here?" they say in unison. Ziva says she asked first. McGee says it was a tie but since "my parents raised a gentleman and yours raised a killer....I was defragging my computer." Ziva spots that the detritus on McGee and Gibbs' desks indicates that they were there all night. She is outraged at being left out of work: "Are we a team, McGee?" She admits she is worried about Tony not turning up at the bar last night as he had promised he would. She is so aggravated that she begins to threaten Gibbs and McGee with what she will do unless they tell her what is happening...but then she pauses, smiles like a cat, and purrs that McGee will tell her...eventually. Gibbs and McGee exchange raised eyebrows. Gibbs tells her nothing, but we know that he had McGee hacking the CIA's computers for information on Jenny as a roundabout way of getting information on the Frog.

We cut back to the limo which has to make a quick stop at Jeanne's hospital: she leaves Tony to the Frog's inquisition whilst she does her work. Frog asks whether Tony is going to break his daughter's heart. Frog is still treating Tony as DiNardo.

Back at NCIS HQ, the Director sneaks past Abby, who is asleep on the lab floor, with the AFIS database flashing up a fingerprint match, showing that Jen's dead father left fingerprints on a whisky bottle in Jen's study. Jen silently deletes the search result. The computer's noise wakes Abby, who is disoriented at the abrupt awakening. While Abby gabbles, the Director receives a phone message from Tony indicating that his cover is blown and he is in trouble. The Director tells Abby that AFIS did not find a print match and then heads upstairs to Gibbs' team. Abby checks her computer, finds the erased file and realizes that it is bad news.

Just as Gibbs is informing Ziva that the CIA is after the Director, the Director arrives and finally explains that Tony is in trouble and that he has been dating the Frog's daughter. Gibbs, the keeper of secrets, is unimpressed at having been kept in the dark. McGee uses Tony's cell phone as a GPS tracker and realizes that Tony's car is on the move.
The Director orders him to get visual contact and use MTAC (Multiple Threat Alert Center where one can watch one's enemies via satellite or security cameras).

In MTAC, the team are tracking Tony's car and discovering how deep Tony's cover was (the car is registered in DiNardo's name, his cell phone message is for Professor DiNardo). They identify his car and watch police traffic cameras to track him. Thus they are watching when the car explodes. The team is dismayed as they believe that Tony has perished in the explosion.

We cut to the team's arrival at the bomb site. With sombre faces, they pull on the latex gloves and start on the crime scene protocols. McGee decides to believe in miracles and hope that it is not Tony. We see the car has mostly disappeared (it was a soft-top convertible) however, the driver is sitting at the wheel, although burned to utter crispness. No fingerprints (but internal organs intact). Ducky makes initial observations and realizes from the Director's responses that the Director blames herself. He asks Gibbs whether she should, but Gibbs does not answer.

We cut to Gibbs in Abby's lab as she unpacks the evidence from the bombsite, including Tony's ID. Abby insists that, until proven otherwise, she refuses to believe that it is Tony. She seeks reassurance from Gibbs which she does not get. Gibbs then notices the whisky and crystal glass he had seen at Jen's house and demands to know what they are doing there. Abby confesses the Director swore her not to disclose where they came from but search results revealed her father's prints on them. Gibbs goes and confronts the Director: he points out that she is likely to be unable to make reasonable decisions when she is polygraphed by the CIA on Monday. The Director refuses to believe her father is alive. She refuses to admit the Frog operation was her revenge for her father. Gibbs warns her she may want to skip the polygraph test on Monday.

In the squad room, McGee is obsessively going through the images from the traffic camera, leading up to the car explosion. Ziva is convinced that Tony is dead. But McGee keeps looking for whether Tony was being tailed by someone. Ziva spots something else.... Tony was tailing a limo.

Down in Ducky's autopsy room, he and Palmer are trying to ID the body. The blood type matches Tony's blood group. But then, whilst dictating his report to Palmer, Ducky realizes that the victim's lungs are healthy with 'minimal scarring'. Ducky wonders how this could be Tony, because when he had had the plague which caused pneumonia (in 2x22 SWAK) it caused more than "minimal" scarring of Tony's lungs.The dead body 'never had the damn plague!', much to Ducky and Palmer's delight. Ducky departs to the squad room to report this to the team. But if it is not Tony, who is it? And where is DiNozzo?

Whilst the team swings into action to work out the ID of the dead man, they are interrupted by the arrival of Trent Kort, the CIA agent who was undercover, working for the Frog. He has mislaid his arms dealer and he is angry with Tony and the Director for jeopardizing operation Lodestone. As Kort is leaving, Tony steps out of the lift. Tony gets a hostile reception from Kort who instantly finds the NCIS teams' guns trained on him as he threatens Tony. Tony is insouciant. He cracks one-liners and even implies that he "broke wind" in the lift and that it is now smelly so Kort should use the stairs. Kort leaves, disgusted.

In the Director's office, Tony is shown the explosion footage. He points out that it was more exciting live. He tells the story of his day to the Director and Gibbs. Tony theorizes the bomb was aimed by the CIA at Tony (because Kort has a hair trigger and doesn't play by the rules). When the Director asks what Jeanne said when she found out the truth, it is clear that Tony is angry his relationship with Jeanne is falling apart. The Director is astonished that he could have thought it might have ended any way other than badly. Tony refuses to share personal information despite the Director's demands. Gibbs smiles (ever so slightly, but noticeably) at this Gibbs-like reaction from Tony at a personal intrusion from Jenny.

In the squad room, Ziva (exhibiting her infallible intuition over all matters Tony) is on the phone trying to find Jeanne for Tony. Tony arrives and starts to phone the hospital looking for Jeanne: Ziva updates him that Jeanne has told the hospital she won't be in. Abby rushes in to greet Tony. Everyone has to start giving back Tony's property they had nicked when they thought he was dead (his Mighty Mouse stapler (Ducky), his letter opener (Ziva), and his American Pie coffee mug (Palmer)).

Discussion of the bomb leads the team to surmise that perhaps the bomb was meant for Jeanne, who ought to have been getting a lift home from her night shift with Tony (they would normally eat breakfast together after he picks her up). Tony and Ziva go looking for Jeanne at her flat. She has moved out. You can see Tony's heart sinking, with every step he makes further into the empty flat.

The Director arrives home at the end of a long day. She is surprised when the Frog calls on her phone and then discovers he is already in the house to have a meeting. So too is Gibbs (whom the Frog hadn't realized was there). The Frog offers information in exchange for protection, knowing that his enemies are after him (but who is his enemy? The CIA? "Another arms dealer, perhaps"?) Jen realizes that the Frog has been in the house before: he admits it is where he paid her father the bribe. "No", says Jen, "You killed my father when he refused that bribe." She reaches into her desk but the gun she pulls out is not loaded (Frog or Gibbs preempted her). Jen rejects the Frog's offer of information in exchange for protection, expresses the wish his enemies kill him and the Frog says he hopes his daughter, Jeanne, will be as loyal to him as Jen is to her father and leaves. Gibbs accuses Jen of neglecting her duty. She is scathing and tells him "you go get a warrant" because she won't. Gibbs hands back the bullets to the gun and asks whether she really would have killed the Frog. She merely says "I guess we'll never know" so he leaves.

In Jeanne's apartment, Ziva finds Jeanne's sealed note to Tony and hands it over. He reads. (this note becomes significant in Episode 5.02). He asks whether Ziva has ever lied to someone she loved. "Yes" she replies. He asks, "How did they take it?" They never found out is her answer and Tony says Jeanne found out. He tells how he told her (flashback sequence to after the bombing, Tony and Jeanne take refuge in a park and sit on a bench. The Frog watches from the entrance to the park, out of earshot. Jeanne realizes that the bomb was meant for Tony... and her, but why? Tony demands her to tell him she loves him and she says she does but she doesn't understand...Tony seemed so different last night with the gun (shooting the druggie) and today with the bombing, it is like she doesn't know him anymore. He admits he is an NCIS agent. But she doesn't know what she is supposed to have done. Tony indicates that it is her father he was pursuing. Why? Ask him. She is distraught. (He is not a happy bunny.) Back in the flat, Ziva offers to go find Jeanne, but Tony says 'She doesn't want to be found.' Ziva leaves. Tony sinks onto the sofa and, from there, down to the floor, arms resting on knees, staring at the letter in his hands. He is a most unhappy bunny.

Next morning in the squad room, Ziva notes that Tony is missing: with permission or just missing? Gibbs merely remarks that there is always more work to do with one man short. McGee has traced a yacht registered to the Frog. The warrant has arrived so they go off to execute it and arrest the Frog. They search the yacht but he isn't there: a coat indicates that he had been there, though. They leave, saying that he will turn up or someone will find him.

As the team leaves, the camera pulls back away from the boat, across the water. And then we see, in the water, the Frog. Dead. Bullet hole in the head. His body sinks. No one sees...except us. Shhhh. Credits roll.