A recap from last season reveals the depth of Tony and Jeanne's relationship, as well as the fact that La Grenouille had Kort spying on them. Tony and Jenny discuss their involvement in a top-secret operation involving La Grenouille. Gibbs learns that NCIS is being investigated because of Jenny's personal vendetta. Jeanne notes how well Tony shot the gun at the man who held them hostage in the hospital morgue. McGee discovers a secret CIA operation called "Lodestone" that involved La Grenouille and Colonel Shepherd, who committed suicide 12 years ago. However, Jenny heard from an old friend that her father is really alive. She discovers a bottle of Scotch and a tumbler in her study, then brings it to NCIS for Abby to check the prints. Opening the door to a limo, Jeanne surprises Tony with an introduction to her father, who happens to be La Grenouille, and he greets Tony by calling him Professor DiNardo.
In her office, Jenny is having a dream about her father preparing to kill himself. She is running to find him, and then he is shot by La Grenouille.
In the limo, Tony, Jeanne and her father head to breakfast. La Grenouille looks suspiciously at Tony and says he has many questions. Tony is clearly uncomfortable. Jeanne confronts Tony about shooting the man in the morgue. Tony gets Jeanne to tell her father about it while he discreetly tries to make a phone call. Jeanne's beeper goes off saying she is needed back at the hospital for a signature.
At NCIS, the elevator doors open, and McGee and Ziva run into one another. Both ask, "What are you doing here?" Ziva quickly says, "I asked first." McGee believes that it was too close to call but since he was raised to be a gentleman and Ziva was raised to be a killer, he responds, "I was de-fragging my computers." Ziva doesn't believe him. She sees food on McGee's desk and notes he has been here all night. She admits she's worried about Tony, as she still can't get a hold of him. He's been MIA since last night. Ziva then notices food on Gibbs's desk and wants to know what they're keeping from her. Gibbs enters, and Ziva declares that teams aren't supposed to keep secrets.
Back at the hospital, Tony wants to go in with Jeanne, but she insists he stay with her father. They walk to get some coffee nearby.
Jenny enters Abby's lab to find Abby asleep on the floor and the computer beeping that it has a match on the prints-Colonel Shepherd. She quickly cancels the search, which wakes up Abby. Stuttering, Abby apologizes for falling asleep. Jenny's phone rings, and she realizes that it's a call from DiNardo that is quickly dropped. She tells Abby she can go, and Abby asks if they got a match. Jen lies and says no, then leaves. Abby turns to her computer, and a message pops up asking, "Do you want to delete search results?" Confused, Abby clicks no, and Jenny's father's picture and profile pop back up. Stunned, Abby mutters, "This is not good."
In the squad room, Ziva is asking why the CIA is after the director. Gibbs says, "You tell me," and Ziva realizes aloud that the CIA is protecting their asset-La Grenouille. Ziva then asks if the director knows as the Jenny walks up and says, "Know what?" Thinking fast, McGee says, "That it's Saturday, and we're all here on our day off because we love our jobs." Ziva adds, "Except for Tony who is missing." Jenny then asks McGee to triangulate a cell number. Gibbs asks if Tony is in trouble. Jenny replies by informing them that Tony's girlfriend is La Grenouille's daughter. Shocked, McGee asks, "He's been on assignment?" Gibbs is upset that Jenny kept it from him and wants to know what's going on. Jenny says that Tony contacted her using his alias's cell, which was a preplanned signal that his cover might be blown. Jenny wants the position sent to MTAC along with satellite coverage.
Meanwhile, Tony and La Grenouille are having coffee as they wait for Jeanne. La Grenouille, or Rene, wants to know what Jeanne told Tony about her father. They both talk about loving Jeanne, and Rene wants to know if Tony will break her heart. Tony replies that he doesn't plan on it. Jeanne comes out of the hospital saying that they need to leave before she gets called back again. Tony realizes he must move his car. Rene says to stay close so they don't lose him. Tony gets into the car.
At MTAC, the team is tracking Tony through the traffic cameras. They are having no luck calling his cell phones. Gibbs asks how deep his cover goes, and Jenny replies that it's deep enough to protect him from the kind of scrutiny La Grenouille would implement. Gibbs threatens, "You'd better hope so." They observe that Tony doesn't appear to have anyone tailing him, and Gibbs suggests that maybe Tony is doing the tailing. As they watch Tony's car turn the corner, they watch it explode. Horrified, Jenny exclaims, "Oh my god!" Ziva whispers, "Tony!"
The team arrives at the scene of the explosion and grimly approach. Car rubble litters the street. With a pained expression, Gibbs stares at the body behind the wheel. Gibbs calls McGee over to start taking photos. Jenny stares at the wreckage, then notices a timer device. Ducky says, thankfully, the shockwave would have killed him before the fire. Jenny asks Ducky about identification, and Ducky says that they height, weight and general build are a match, but they'll have to get his dental records since fingerprints are out of the question. Ducky asks Jenny, "Is there any chance it's not Tony?" Jenny replies, "None that I can think of," and walks away. Ziva recovers Tony's ID and shield from the car.
Back at Abby's lab, Abby has the remains Tony's personal effects spread out before her. She's rambling on to Gibbs that regardless of what the evidence says, Tony's not dead until Ducky says it's him. As Gibbs goes to leave Abby to her work, he sees the bottle of Scotch and the tumbler that Jenny brought to Abby for prints. He confronts Abby about it, and Abby says that the Director brought it in and swore her to secrecy. Upset, Gibbs asks, "Any other secrets you can't tell me?" Abby says no since the Director didn't ask Abby to keep secret the fact that Jenny lied when she said there was no match when there really was. Gibbs asks, "Who was the match?" "Her father," replies Abby. Gibbs says that's impossible since her father is dead. Abby argues that the print is a 10-point match, meaning that it's a new print, so he can't be dead.
In Jenny's office, Jenny tells Gibbs that someone is trying to convince her that her father is still alive. Gibbs tells her about the polygraph scheduled for Monday is because the CIA is targeting her. Jenny isn't worried. Gibbs asks, "If they ask about your father?" to which Jenny replies, "He's dead." Gibbs then asks her if she knows about Lodestone, a CIA black op focused on arms control and weapons proliferation. Jenny admits that her father's job at the Pentagon was in weapons control, and he was under investigation for accepting a bribe when he was killed. Gibbs counters, "Coroner said he took his own life," to which Jenny responds, "He was murdered." Gibbs wants to know if she has any proof, and Jenny says no, but she knows who killed him. Upset, Gibbs demands, "The same guy you sent one of my agents after?" Angrily, Jenny retorts, "One of MY agents." As Gibbs turns to leave, Jenny tells him that he's wrong if he thinks she's obsessed with La Grenouille because of her father. Gibbs comments that she should skip the polygraph on Monday.
McGee keeps watching the explosion, realizing that Tony wouldn't have carried his ID and gun on him since he was undercover; he would have stashed them in his car. The presence of these items does not mean that Tony was in the car. McGee remembers that Gibbs wondered if Tony was tailing someone. Ziva and McGee spot a limousine that Tony appears to be following.
In autopsy, Ducky is removing shrapnel from lung tissue. Palmer reads that the blood test results match Tony's type-A+. Ducky comments that 34% of Americans have that same blood type. He dictates notes to Palmer on the condition of the lungs, noting that they have minimal scarring. Pausing, he realizes that these lungs could have never had Y. pestis, the pneumonic plague. He exclaims to Palmer, "He never had the plague!" Smiling, Palmer repeats, "He has never had the plague!" As he leaves autopsy, Ducky turns and repeats, "He's never had the damn plague!"
Ziva has connected the limo to La Grenouille and realizes that Tony may have been following him. Ducky enters and says no; it wasn't Tony. Tony had contracted the plague and almost died from pneumonia, which severely scarred his lungs, unlike the lungs of the body in autopsy. Jenny asks, "If it's not Tony, who is it?" Gibbs adds, "And where is DiNozzo?" Kort walks in and wants to know where Tony is. Jenny wants to know why he's looking. Kort admits that La Grenouille flew into D.C. that morning, and now they can't find him. He wants a private briefing in Jenny's office, but Jenny refuses saying she'll decide what briefing he gets. Kort says she's jeopardizing the most long-term operation of the CIA. Gibbs interjects, "Operation Lodestone." Kort insists, "You weren't read in for Lodestone," and Jenny replies "So read us in." Leaving, Kort threatens, "This won't end well for you." The elevator door opens, and Tony grins at Kort and asks, "Hey my car blew up this morning. Did you do that?" Kort grabs Tony and shoves him against the elevator, asking where he went with La Grenouille. Tony looks over Kort's shoulder and clears his throat. Kort looks, and sees Gibbs, Ziva and McGee with their guns drawn and pointed at him. He lets Tony go, and Tony taunts, "Happy frog-hunting! You might want to take the stairs. I had a little upset tummy this morning. Phew!" The elevator doors close, and Tony turns to the team and grins, "What, no balloons?"
In Jenny's office, Tony is bringing Gibbs and Jenny up to speed. He tells them that La Grenouille was waiting for them when they left the hospital. "It was her surprise, I guess. Meet the parents, part 2. I hate sequels." Tony surmises that Kort blew his cover to La Grenouille. He tried to get away by getting in to move his car, but Rene convinced him to stay with them by calling him Agent DiNozzo. One of Rene's bodyguards, Henri, took Tony's car and cell phones and Tony watched his car blow up from the limo. Rene assumed he was the target, but Tony figured it was himself for pissing off the agency lately. He says the bomb blew away a lot of things. Jenny asks if he thought that things would end any other way with Jeanne. "You mean, other than badly?" Jenny reminds Tony that he wasn't supposed to fall in love. Sarcastically, Tony retorts, "Thank you so much for that, Director. I'm going to keep that in mind for next time. Wait a second! There's not gonna be a next time!" Jenny wants to know what Jeanne said. "Nothing I'm going to tell you." Jenny presses him, but Tony insists, "Nothing you need to know, Director." Gibbs looks proudly at Tony for standing up to the Director. Tony says that Rene dropped him off at the front gate and drove west, very fast. Rene doesn't think he has a future, and he wants out, which explains why Kort is desperate to find him. The CIA is about to lose their most prized asset. Tony says Rene will be calling to set up a meeting because NCIS is the only agency he trusts.
Back in the squad room, Tony slaps McGee on the head. Puzzled, McGee asks, "What was that for?" "Believing I was dead!" Tony replies. McGee insists that he never believed Tony was dead, but Ziva did. Ziva asks if everything is cool with the director and Gibbs. Tony replies, "Beyond cool. Almost icy." Tony is dialing his phone while asking if anyone called for him. Ziva says no and that Jeanne isn't at the hospital. She told the ER she was leaving for a few days and didn't say where she was going. Ziva asks Tony if Jeanne knows, and Tony says, "She knows." Abby runs in and hugs Tony, exclaiming that she never believed he was dead despite everyone else giving up on him, even Ziva. Tony then realizes that Ziva has his letter opener. He asks about his American Pie coffee mug. Abby tells him Palmer has it. "Mighty mouse stapler?" "Ducky." Ducky pops over the divider behind Tony's desk and returns his stapler, saying that he never really believed Tony was dead. Abby then tells Gibbs that she knows who made the bomb, not really who, but why. The bomb-maker was the same one who set off bombs all over the world to kill other arms dealers. They realize the bomb was meant for Jeanne, the daughter of an arms dealer since Tony would pick her up every morning. Tony and Ziva leave to look for Jeanne.
Jenny walks into her house and answers her cell phone-it's La Grenouille. He wants to meet her. She says tell me where and when. He appears before her and says, "Now, in your study." Rene compliments Jenny on her pursuit of him; he really liked Tony. Jenny asks him what he wants, and he replies that he wants sanctuary, asylum, whatever you call it, in return for information on the arms trade. Gibbs appears and asks if he's wanting protection from the people who tried to kill his daughter. Rene says yes, but she's safe for now. Gibbs wants to know what this has to do with Lodestone. Rene says the CIA wants to make him the biggest arms dealer. Gibbs realizes that Rene will control the illegal arms trade, and the CIA will control him. Rene says that was the idea until NCIS came along, and someone else found out. Now he can no longer trust Kort and the CIA. Jenny interjects, "This isn't the first time you were in this study." Rene agrees and says he used to meet her father and that her father was a good man with a conscience that got the better of him. Jenny asks, "Do you believe the story about the bribe?" Rene replies, "It's not a story. I paid him." Angrily, Jenny exclaims, "No, you killed him," as she pulls out her gun, "because he wouldn't take it!" Gibbs tells Jenny that the gun isn't loaded because Rene beat her to it. Rene insists that he needs protection. Jenny shoves the gun at him and tells him to protect himself. Rene tells her she is signing his death warrant, and Jenny says, "Twelve year overdue." Rene leaves. Gibbs tells Jenny that she just let her personal obsession get in the way of her duty. Jenny replies that that's crap, and he knows it. They had no warrant. Angrily, Gibbs tells Jen to get a warrant, and she fires back for him to get it. Gibbs asks Jenny if the gun wasn't loaded and he hadn't been there, would she have pulled the trigger. Jenny replies, "I guess we'll never know." Gibbs pulls the clip out of his pocket, lays it on the table and leaves.
At Jeanne's apartment, Tony reads a note that Jeanne left him. Trying to cover his emotions, he asks Ziva if she's ever lied to someone she loves. Ziva admits that she has, but that person never found. Tony tells her how he told Jeanne after the car blew up because Jeanne realized he was someone else. Ziva says she'll put out a BOLO, and they will find her. Tony says that she doesn't want to be found. As Ziva leaves, Tony sits on the floor.
The next day, Ziva is trying to get a hold of Tony, saying that if he was taking time off he would have told them. Gibbs enters and says Tony is taking time off. McGee has discovered a yacht that was rented by La Grenouille, and he also learns that someone has been staying on it recently. They all leave, with a warrant this time. Upon arriving at the boat, the search it but come up empty. However, Gibbs does find La Grenouille's trenchcoat, so they know he was there. As they leave the boat, McGee says they'll catch up with him eventually, to which Ziva adds, "Or someone will." "One day," adds Gibbs.
The camera zooms out from the boat to the water to show La Grenouille with a bullet in his head, sinking.