Gibbs and Tony inspect the hallway where we last saw EJ grappling with P2P.
They find the wall of photos and then EJ's team member Cade, who is badly hurt. Levin didn't make it. Tony wants to go find EJ, but Gibbs tells him to stay with Cade.
Gibbs goes to the parking lot, gun drawn. He peers into a car. He sees plastic wrap peeking out of the trunk. EJ is wrapped up inside. He rolls her over. She's still breathing.
Back at NCIS, EJ is in shock. Cade is in surgery, someone's notifying Levin's family in Chicago. Duckie and Palmer are with his body.
P2P keyed a phone number into the side of the car EJ was found in. It's a secure blocked government line. Ziva looks at it and recognizes it as Ray's cell phone number.
Gibbs tells her to find him and warn him.
Vance reads up on Operation Frankenstein, the CIA op that created P2P, also known as Jonas Cobb.
In the bathroom, EJ furiously tries to get rid of the ink P2P drew across her neck instead of slitting it. She doesn't understand why he let her leave. She blames herself for her team getting hurt. She wonders if all this would have happened if anyone but her had been on the case. Tony tries to reassure her and cautions her not to let P2P get in her head.
Gibbs visits Duckie in the morgue. He thinks Cobb used Frank's gun on Levin. Cobb's trying to punish people who turned him into Frankenstein.
EJ comes down. She wants a moment to pay her respects. They leave her alone with his body. She holds Levin's hand, then examines his wrist. She takes out a knife and makes a tiny slit. She squeezes a tiny electronic pellet out from under his skin and puts it in a small plastic specimen jar. She takes it.
Ziva can't reach Ray. P2P knows he;s on the case and she's worried about him.
Secretary of the Navy Phillip Davenport (Jude Ciccolella) comes to NCIS and barks at Vance that it better be important. Gibbs says with an agent wounded and another dead, nothing's more important.
McGee's waiting for Abby in her lab. She spent the night at the hospital at Cade's bedside. McGee picks that moment to be jealous and ask if they're more than friends. She announces it's time to go home. He wants to go with her to protect her.
Ziva tries to reassure EJ there's no rhyme or reason to agents dying on the job. EJ says it's her fault, but Ziva says it was just Levin's time.
Tony calls Ziva with info from Agent Kort on a DC hotel where Ray is staying. EJ wants to go with her, but Ziva says shes going to get her boyfriend and he'll be staying with her instead of a safehouse.
At the hotel, Ziva knocks on the door. She walks in when it opens. Instead of seeing Ray, Cobb is waiting for her. He knocks her out.
Sec-Nav Davenport tells Vance to deal with the situation and then asks if he's up to it. Vance says since Eli David was here and since he got here, things have been different. He says things have gone wrong. Vance takes out file marked confidential. Davenport doesn't want to talk about Frankenstein, but Vance flips a switch and assures him the room is secure.
Gibbs looks at an old letter from Mike down in his basement. In it, he says he's only got a few months left with his lungs. Gibbs works on a flower inlay on a piece of wood.
Gibbs gets a call from Tony.
Back at NCIS, Tony tells Gibbs about Ziva going to Ray's hotel room. He's unconcerned until he sees Ray is standing there. He hasn't checked in yet. They can't reach Ziva. EJ tries to blame herself, but Gibbs nips her martyr routine in the bud. Ray assures them Kort didn't mislead them.
Gibbs learns Kort, or Agent Eyepatch as Tony calls him, is already in the building.
Vance, Kort and Davenport meet in Vance's office. Kort reminds Vance that Operation Frankenstein was his idea when he was in the War College. Vance says it was flawed from the beginning and should have been aborted. Davenport defends the idea. Vance blames Kort for pushing Cobb too far.
Vance says it's not Gibbs and Barrett's fault. For once the weight does not fall on the bottom of the pyramid. This operation was your call, accept it, Vance tells Davenport.
Gibbs storms up to the office and tries to bust in like always, but it's locked down tight. Instead he takes the secretary's phone and calls in.
He tells them Ziva is missing based on info from Kort. If she gets hurt, you answer to me, Gibbs says.
Kort asks Vance if Gibbs is threatening him.
If he isn't, I am, Vance says.
At the hotel, Tony can't hide his concern. EJ says everyone is worried. It's just different for some of us, he says.
EJ wonders what that means when suddenly Cobb strolls through the hotel room door, with his arms raised. He gets down on his knees and surrenders.
Back at NCIS, EJ thinks Cobb is playing them. Tony cites Rule 16: If someone thinks they have the upper hand, break it.
Gibbs joins Cobb, who snorts with derision. He thinks Gibbs is acting proud. Gibbs says there's nothing to be proud about since Cobb gave himself up. Cobb says his work was almost done.
He mentions Samson, who he says EJ wrote about in her psych profile of him.
Cobb tells Gibbs about a boy whose father was a captain in the navy, who had a horse named Samson who needed to be put down. Instead of calling the vet, the captain shot the horse to teach a lesson.
Gibbs asks where Ziva is.
Now what kind of lesson would you learn if my actions were humane? Cobb says.
You failed as a navy officer, you were an embarrassment to the CIA, a disappointment to your dad and you want to teach me a lesson? Gibbs says.
Tony demands information from Ray. He says Frankenstein was a legitimate CIA operation, but there was a similar program for the private sector. Kort skimmed money off the top. Ray suggests Cobb would only give himself up so easily if there was something specific he wanted at NCIS.
Tony confronts Kort, who says he has no idea how high this goes. Certain people had a lot to gain from this project, Kort says.
He tries to get Tony to think four moves ahead like P2P.
Abby finds the blood on Cobb's hands is Ziva's. There was concrete dust from where Cade and Levin were shot. She also found sheet metal rust and homeopathic oils that help with muscle aches in people. What if they weren't people? Gibbs says.
McGee confirms the oils are used on liniments for horses. McGee finds a record of the Cobb family farm.
Gibbs tells EJ she can't go, people upstairs want her benched.
He tells her he knows the Sec-Nav is her uncle and has from day one.
She insists she got where she is on her own. He doesn't think so.
At the Cobb farm, they find the house deserted. They inspect the barn, with a stall marked Samson. Theres a toy monkey clapping.
They find Ziva tied up in the next stall. Shes got a cut on her head but is OK. She quickly tells them her kidnapping was a distraction. Cobb needed to get them all out and get into NCIS.
Vance and Davenport have security. Gibbs points out his niece EJ doesn't. This is news to Tony.
Back at NCIS, an agent leads Cobb onto an elevator with EJ and Palmer, who couldnt be more nervous. EJ asks Palmer about his news. He's getting married in the spring.
When they get off the elevator, Cobb knocks out the agent holding him with a head butt, kicks EJ to the floor and jumps over his cuffs so his hands are in front. He puts them around Palmer's throat and tells EJ it's round two. They're going for a drive in the ME van.
The team is back upstairs and tracking the ME van. Tony is still smarting EJ didn't tell him about her uncle.
Ziva defends keeping quiet about powerful relatives, something she understands having a father who's the head of Mosad.
Up in Vance's office, Davenport questions the plan. Gibbs thinks Cobb had the chance once to hurt EJ and didn't. He's showing them how humane he can be, Vance says.
They found a note saying they'll be waiting at home.
It's the building where Frankenstein took place, where Cade and Levin were shot.
Davenport tells Vance certain private jobs were taken as political favors neither the CIA nor Navy officially authorized. Kort handled them.
Davenport announces he's submitting his resignation as soon as this is over. Let's take care of this son of a bitch, he announces.
Davenport walks into the Frankenstein building alone, wearing a bullet proof vest. He finds Cobb waterboarding his three captives. He says he's training them. His third student is Kort. Cobb knocks him out.
Cobb holds his gun to EJ's neck, saying she's a good agent. Cobb waits for the other agents. Vance and Gibbs come in.
I thought I was being trained to do what was right, Cobb says.
Davenport says they can talk about things and he wants to help.
Gibbs looks toward the ground. Palmer gets the signal. He waits.
Liar, Cobb says. EJ and Palmer both duck. Vance, Gibbs and Davenport fire. Cobb is blasted out through the window. He falls several stories and lands on a car below, toast.
EJ packs up her things at work. Cade has been reassigned to Washington state, to spend time with his family while he heals. McGee tries to appear sad to see him leave.
EJ tells Tony shes quitting, too. You can have Rota if you want, she tells him.
I think I'll stay put, no sense walking away from a good thing, he says.
Is that a compliment, DiNozzo? Gibbs asks.
No sir, boss, sorry. Never, Tony says.
EJ announces she's thinking about sticking around DC. Tony suggests maybe they'll bump into each other. She says it's possible, but seems to mean see you tonight.
Gibbs tells her to come back any time.
Ziva opens a jewelry box from Ray. It's empty. He tells her to consider it a promise. He says he has to work outside the country for a while. She doesn't want him to go. He says he has to.
Is this good bye? she asks.
How do I know? You gave me an empty box.
I gave you a promise, he says.
Ray gets a text: Kort in Tel Aviv. Handle ASAP.
He tells her it's nothing.
Gibbs serves as a pallbearer for Mike Franks at his military funeral at Arlington.
Everyone is there.
He's buried in a fine, handcrafted wood coffin. We recognize the wood details Gibbs has been working on all season. Franks knew he'd need it and must have asked in the letter.
Vance talks to the new Secretary of the Navy, Clayton Jarvis (Matt Craven). Theyre old pals. Jarvis mentions DiNozzo, saying hes spoken to him twice already.
Tony joins them. Jarvis gives Tony clearance to discuss a black op, saying no one else needs to know. Vance is concerned but Jarvis barrels on. He says an agent in NCIS is selling top secret intel and they need to be dealt with.
Jarvis gives Tony the file. He looks at it and is stunned and concerned, but then regains his straight face. That's who youre handling, Jarvis says. Any questions?