Two little boys are biking and kicking around a soccer ball in a suburban cul-de-sac, complaining that their neighborhood is boring. Suddenly, they hear a crash, and rush over to the next street, where they see a pick-up truck has had an accident. One of the little boys rushes and opens the passenger door, worriedly asking the driver if he is alright. The driver is dead--with a gunshot wound through the neck.
McGee cheerfully strolls into the office one morning, and notes that Tony and Ziva are out of sorts, even "surly." "'Surly' you're mistaken," declares Tony, but McGee reminds them that neither of them went to the Navy District New Year Eve party, and it is unlike either of them to miss a party. McGee suggests they are suffering from the holiday blues, but Tony shrugs it off, asking Ziva if she has heard from C.I.Ray. She deflects the question, asking him if he had met up with his old high school flame, Wendy. "Something came up," Tony tells her. "Yeah – a U-turn," McGee smirks. Tony responds that he doesn't have the blues, exactly, but maybe the blahs. Ziva enthusiastically tells him that if he wants a change, then he needs to take action, but Tony sneers that that is strange advice, coming from someone who has been waiting for eight weeks for a phone call from Ray. As they begin to bicker over who should take action, Gibbs interrupts them--the dead motorist was a Naval officer.
At the accident scene, Ducky determines that the gunshots came from the passenger side of the truck, prompting Tony to observe that the killer was "riding shotgun." The victim is Commander James Barsway. They note that there are no shells on the floorboard, and the witnesses didn't see anyone fleeing the scene. The passenger window was open, which leads them to think that it was a drive-by, where they find a bullet casing near the curb. They find a neighborhood busybody who was peering out of their window and who saw a pretty blonde woman jump out of the victim's truck and run into the woods after the crash – and she wasn't the commander's wife. They interview the commander's wife, who confirms that a woman from the commander's work overseas years ago had called him that morning before breakfast. He dropped everything and had left to help the woman: "He'd do anything for a friend."
The commander had been posted all over the world, and had a reputation for being hard-nosed, but fair. The phone call he received that morning came from a burn phone. In the lab, a hungry Abby who has missed lunch can find no identifying marks on the bullets, but has run an analysis on the commander's GPS and determined that the car had been to the Highway 12 Motor Lodge. Gibbs presents Abby with a sub sandwich as a reward.
Gibbs, Ziva and Tony interview the desk clerk at the Highway 12 Motor Lodge, who has no records of the blonde woman. "She was so terribly pleasant, she was like one of those Star Wars Jedi people:'You do not need to see my ID,'" he mimics her in excuse for not taking the required identification. She had paid cash three days in advance, and the only thing the clerk has on her is her name in the register: Belva Lockwood. Tony is suddenly intent, and grabs the registration sheet, commenting that Belva Lockwood was the name of the first woman to run for President, in 1884. They obtain very blurry security footage that shows the woman getting into the commander's truck, and returning just a half-hour ago. They see her leaving the hotel with her bag, and they head across the road to a truck stop. McGee and Abby are working on clearing up the film, and the rest of the team discovers that a blonde woman in a red coat just hitched a ride with a truck. They stop a truck on its way out. McGee and Abby get an ID on the film at the same time the blonde woman descends from the truck, to everyone's astonishment: It's E.J. "Hi, guys," she says, sheepishly. The team is stunned: "You're alive?" Tony declares.
Ziva, Tony and Gibbs question E.J. as she gulps down dinner--she has been on the run since Cade was killed. Tony is angry: "You left me lying on the ground in an alleyway!" he accuses her. "I thought you were dead," she tries to explain. "You THOUGHT?" he repeats angrily, and she explains that she heard a few days later that he was alive. "It didn't stop you from running, though," he snarls. "I wasn't running, Tony--I was on the run!" "Well, THERE'S a distinction," Tony mocks her. Gibbs breaks up their argument, asking why she didn't trust them to help. She tells them she was trying to protect them against the same person who killed Cade (she had been wearing a bullet-proof vest when they were shot in the alley). They show her a picture of FBI agent Casey Stratton, and ask if he was the shooter that morning, but she says it wasn't. E.J. and Abby come up with a picture of the shooter, and begin to run it through an ID database. Tony asks if she's sure of the description, and E.J. angrily confirms that she would hardly forget someone trying to shoot her at close range. Abby beats a strategic retreat from the tension, leaving Tony and E.J. alone. Tony tells her that he got suspicious when he heard that the commander had been stationed in Naples, given that E.J. had raved about Naples in the past, and that he remembered that she had talked admiringly about Belva Lockwood. Tony is angry that he spent a lot of time looking for her, and she never reached out to them--or to him. She explains that she was frightened, doesn't know why he is after her, and couldn't identify him. At that moment, the computer program finds a match for her sketch.
Ziva is skeptical: "With all due respect for what she has been through, Tony, how could E.J. think that living off the griddle was a better option than having us to protect her?" McGee, too, is skeptical, and Ziva tells Tony that they don't want to see him get hurt--again. "I can handle myself," Tony objects, but even Gibbs is skeptical. The shooter identified by E.J.'s sketch is former Captain Marcellus Dane, dishonorably discharged in 2005 for accepting bribes from military contractors, and subsequently hired by the same contractors as a gun expert. The team tries to make a connection between Dane and the commander, but E.J. objects that Dane was shooter at her, not at the commander. "You'll have to take my word for it," she declares. "Why?" asks Ziva meaningfully. They track Dane's cell phone, which has just been rebooted in downtown D.C. warehouse. They are suspicious, because it is unusual for a paramilitary expert to be that sloppy with their cell phone, but the rest of the team starts out for the warehouse, anyway, pointedly leaving E.J. behind under guard – by Tony.
As they pull up, they see an active crime scene being worked by the local police. They identify themselves and approach a body lying on the ground--it's Dane, who has been recently stabbed and pushed from an upper-story window. Ziva realizes that the killer was the one who turned on the phone, in order to lure them there. Gibbs surveys the crowd, but misses seeing Stratton hiding in the back of the on-lookers.
Gibbs enters an elegant but deserted restaurant, flashing his ID, and approaches SecNav, who is talking to two other men while under the watchful eye of bodyguards. Gibbs asks to speak to him privately, and asks him for a favor: He want SecNav to speak to Sean Latham at the FBI, because NCIS may have a bead on Stratton. SecNav protests that the FBI takes imposters seriously, but Gibbs is referring not to the FBI, but to the Phantom Group in the copy of the photograph with Stratton and Latham in it that he has referring to a clandestine group attached to the Watcher Fleet. Gibbs reiterates that Stratton killed Cade and shot DiNozzo and Barrett. SecNav remembers that Barrett is MIA, but Gibbs corrects him--she's in a safe house with Tony on Old Rag Mountain. Gibbs reminds SecNav that he is the one that brought Latham into the case, and after seeing the hospital surveillance cameras when Tony was injured, Latham should have recognized Stratton, but pretended not to. Gibbs reminds him that Stratton has a locator chip in his arm, and that Latham knows how to find him, and needs to bring him in.
Tony and E.J. enter a disheveled safe house. Tony is talking to Gibbs on the phone, somewhat in code, pretending they are talking about a football game, and how he and E.J. are going to "tailgate" (i.e., they've arrived at the safe house.) As Tony finishes up his conversation with a "good luck tomorrow," E.J. is walking around with a look of distaste, surveying old newspapers, empty pizza boxes and an unmade bed, and comments that his talking is code is a little obvious. Tony points out that they don't know if the phones have been compromised, but now they know that SecNav is on board with the plan. When E.J. asks when the last time the house was cleaned, Tony remarks that "it's called a safe house, not a tidy house. I know that it's a far cry from the luxurious truck stop motor lodge you've been staying at." E.J. is feeling guilty at the deaths she feels like she has caused: Levin, then Cade, then Barnsway. Settling in for the night, Tony tells her, "That which does not kill us makes us stronger. I think Nietzche said that. Of course, the important thing to remember about Frederich Nietzche is that he died in an insane asylum. It's probably not the best way to start a pep talk, huh?" He admits that he's made mistakes, and when he turns to E.J., expecting a comment, he finds that she is fast asleep, exhausted. He gently adjusts the blanket over her shoulder, and settles back for a long night of watching, his hand resting on his gun.
SecNav has asked Latham to meet him at NCIS. He and Gibbs meet with Latham in the conference room, and Gibbs confronts him with the group photo of him with Stratton. Latham protests that it is classified, and asks him to explain about Stratton, and why he didn't admit that he knew him earlier "when he tried to shoot down my best agent". Latham tells them that the man they call Stratton is actually Captain Jonathan Cole, a former Green Beret that Latham recruited into the Phantom program in 2003. Latham refuses to believe that Stratton/Cole is responsible for killing NCIS agents, and SecNav asks Latham to arrange a meeting between him and Stratton/Cole. Latham asks when, and Gibbs tells him the sooner the better, because two of the agents are in a safe house, and less safe the longer Stratton/Cole is out there. Latham agrees to do what he can.
It's early morning. Tony has dozed off, the remains of a solitaire game at his feet, but wakes up abruptly when he hears someone at the door. He points his gun at the door, but it's Ziva. "Room service!" she chirps brightly, carrying coffee and unfazed by the gun pointed at her. "Easy, lion!" she admonishes Tony. Blearily, Tony corrects her: "Tiger, it's 'easy, tiger'." Ziva tells him that his phone doesn't work well in the mountains. E.J. emerges from the bathroom and Ziva offers her coffee and muffins with jam. "You know, Ziva, everything that Tony told me about you isn't true!" E.J. tells her. "I never said . . . she didn't like coffee," Tony finishes weakly as Ziva stares at him accusingly. Tony grumbles that he is feeling the effects of sleeping sitting up, and goes off to take a shower, leaving E.J. and Ziva alone. Ziva tells E.J. that Gibbs had her check her secure email while she was gone, and brings her an email from her mother, whom she hasn't contacted in months for fear of putting them in danger. E.J. thanks her. They relax in each other's company, and E.J. asks Ziva about her plans, after NCIS. "A family?" she inquires. Ziva admits that it's a "maybe," but that it appears increasingly unlikely at the moment. E.J. offers a toast: "To someday."
Latham, walking his dog, meets Cole in a pedestrian tunnel, telling him that NCIS has made the connection between them and wants to arrange a meeting. Latham admits that the business relationship they had selling microchips was very profitable, but it's all behind them, now, and Cole is a wanted man. Cole protests that he can't proceed until his assignment is behind him, but Latham tells him to forget about the girl. When Cole says he can't, Latham becomes angry. "I don't get it, Cole--success has made you, what . . . crazy? Cocky? Or just sloppy?" He tells Cole he won't get DiNozzo and Barrett, because they have them at a safe house on Old Rag Mountain. "You sure?" asks Cole. "Per SecNav--even for a politician, he talks too much," comments Latham. He asks Cole to disappear, "so that both of us don't end up in Leavenworth." Cole nods, and offers his hand. Latham reaches out to shake it, but Cole stabs him in the chest. Gently lowering him to a nearby bench, Cole tells him, "No loose ends, sir," and, taking Latham's dog, nonchalantly jogs away.
In Autopsy, Ducky confirms that Latham was killed by the same knife and technique that Dane was killed by--a knife twisted into both lungs. Ducky has also extracted the deactivated microchip similar to Levin's and gives it to Gibbs to "add to the collection."
Cole is scrambling down a hillside, behind some trees. He quickly unpacks a rocket launcher and aims it at a small, nondescript cabin tucked beside the mountain. Inside the cabin, Tony unpacks a suitcase filled with firearms; E.J. is taken aback at the firepower, but Tony tells her, that "with Cole on the loose, with some Connery paraphrasing, 'Never bring a knife to a gunfight." E.J. guesses it's a James Bond quote, but Tony resignedly corrects her: "The Untouchables. 1987. Connery won a Best Supporting Actor." E.J. gamely tries to continue the conversation: "I liked him in Xanadu," which causes Tony to suppress a shudder. Outside, Cole has his launcher trained on the house, then loads it. Inside, Tony comments that one of these days, he hopes to meet someone who appreciates movies as much as he does – or at least, appreciates the way he appreciates them. "She does, Tony," says E.J. gently. "Who?" asks Tony. "Ziva," E.J. tells him. He laughs. "Agent Ziva David believes that Pirates of the Caribbean is a cinema classic," he scoffs. "I'm not talking about movies, Tony – I'm talking about you. She cares," E.J. insists. Outside, Cole aims his loaded rocket launcher at the cabin door. Tony discounts E.J.'s observation: "What the matter with you? We're co-workers, we're teammates, we have each other's backs." "Exactly!" says E.J. Tony looks down at the gun he is assembling, and quotes. "Surround yourself with people you would give your own life for." Outside, Cole shoots, and the cabin explodes in flames. Gibbs, Ziva and McGee hear the explosion and begin running. Cole quickly packs up and dashes off, leaving the launcher behind. Ziva spots him and yells out that she has a visual, and Gibbs shouts out for her to take the shot. She pursues him as McGee comes up on the other side. They corner him in a stand of trees as Gibbs joins them. Ziva identifies Cole's gun as probably a 50-caliber gun, with limited accuracy. "Seems pretty damn accurate to me," says Gibbs drily, hunkering behind a bolder. A gunfight ensues, and Cole dashes off, herded through the woods to a clearing where the police are waiting. He whirls, and Gibbs is right behind him, gun pointed at his head. "Go for it," offers Gibbs, with a slight smile. Cole considers, and then drops to his knees, putting his gun on the ground and placing his hands behind his head. "I'm sorry for your loss," Cole tells Gibbs with false sympathy as he's handcuffed by Ziva and McGee. "Wrong place, wrong time." Gibbs heaves a sigh: "You got that right." Gibbs makes a phone call--which is answered by Tony. "We're ready, Boss," Tony says. "Game on?" "Game over," answers Gibbs. Tony walks outside of his cabin--a different cabin. "How are you, DiNozzo?" Gibbs asks genially, to Cole's shock. "I'm good--I take it Latham took SecNav's bait?" "Yep, gave up Old Rag Mountain." "That's 20 miles east," laughs Tony. "Jarvis must be one hell of a liar." "Uh-huh," agrees Gibbs, "glad he's lying for us." Ziva and McGee escort Cole away.
At the cabin, E.J. joins Tony on the porch. "Time to move?" "No, time to stop running," Tony tells her. She takes a deep breath of relief.
Back at the office, Tony invites E.J. to join him and Ziva for a drink, but she declines, saying that she is on her way to visit her mother. He offers to give her a ride, but she tells him that SecNav has sent a car for her. Tony is impressed. "So c'mon, you can say it," he tells her with a smile and outstretched arms: "I'll miss you most of all, Scarecrow!" E.J. grins at him. "Wizard of Oz," she correctly identifies the quote. Tony grins back. "Look at you, how far you've come! I'm proud of you." "We've been down this yellow brick road before, Tony. Thanks again," she says, giving him a brief kiss on his cheek as she leaves.
In Interrogation, Gibbs sits down at the table with Cole, who asks if the handcuffs are necessary. "You should be flattered," Gibbs tells him. Cole defends the Phantom project and his role in it. Gibbs acknowledges that the Phantom project took out a lot of bad guys, but it doesn't excuse his latest actions. Cole suggests that Gibbs is more like him than he thinks. "I don't kill innocent people for money," retorts Gibbs. "No? So why DO you kill innocent people?" Coles says knowingly as he begins to hum "South of border, down Mexico way . . . that's where I fell in love, and the stars above came out to play . . ." Gibbs stares at him implacably.
In the office, Ziva is shrugging her coat on and notes with a small smile that E.J. is gone. "And safe, for a change" agrees Tony. Ziva asks where she has gone, but Tony just tells her that she has gone "somewhere quiet, with someone she can count on--hopefully." Ziva picks up on the qualifier, and agrees that that's the rub--finding someone you can count on. Tony asks if there's problem with Ray, but Ziva doesn't want to discuss it. "At least E.J. and I parted as friends," he tells her, "Agent Cruz appears to have communication issues." "Yes, and I'm losing my patience," says Ziva with an edge in her voice. "As you well should!" Tony says encouragingly. Coming over to her desk, he leans against it and tells her, "You know, you and I have a lot in common, in that respect." "You think?" Ziva laughs, but Tony only smiles slightly. "I don't think – I know." She looks at him speculatively for a moment, looks away for a moment and then returns her gaze to him. "Well, then, I am . . . grateful . . . to have someone in my life that is as romantically dysfunctional as I am!" she tells him. "Agent David . . ." Tony says, drawing out her name, "do you really consider me to be in your life?" Ziva, startled, looks at him closely with a nervous smile. The gazes become searching . . . and suddenly, her phone rings. She glances at it, and sighs. It's Ray. "No!" exclaims Tony in disbelief. "Seriously!" agrees Ziva. "I mean, what should I say?" "Say, 'hello'," Tony suggests, nonchalantly tapping his sunglasses against his chin. "Hmm. OK. Excuse me," she murmurs, as she squeezes closely past him to leave her desk. He doesn't move, forcing her to press against him as she edges out, but gives her a small grin and watches her thoughtfully as she walks over to the windows and answers the phone.