A guy talks to his wife on the phone, making excuses for not coming home last night. He walks around frantically in a park, then sits on a bench and makes another call. "I'm starting to really lose it here. I can't keep lying to my wife, it's killing me. We need to end this," he says. As he tells the person on the other end where to meet him, a gloved hand holding a gun sneaks out from behind a tree and shoots him dead.
Tony comes to work, irritated with his dad for over-doing his birthday plans and making Tony foot the bill.
McGee remembers his dad assessing a special card he made for him one year and giving it back, saying he could do better. His dad was a crusty navy admiral who believed in tough love.
Gibbs comes for the body of the week, a dead navy officer downtown.
He was shot in the head. He's Lt. Paul Booth. Ziva found a badge with his name on it. His fingerprints are burned off. Tony finds McGee's business card on the victim.
Back at the office, McGee can't place him, but the victim had his eight-year-old business card. Booth served two tours overseas and had a good record. He taught math at a university, but recently cut his schedule down to one class a week. The employee badge he had was for Telis Research. McGee hacks in and finds Booth was an analyst and reported to the company VP John Westfal (Sam McMurray).
Gibbs talks to Mrs. Booth, who is very pregnant. She tells Gibbs Paul was anxious when they spoke. At first she thought it was an affair, but a few weeks ago he came home late and she saw a car parked across the street watching him.
She saw the man again the last two nights.
Ziva and Tony visit Westfal at Telis. Booth's wife didn't know he worked there. Westfal won't tell them what Booth was working on.
Down in the morgue, Palmer's phone keeps ringing. The wedding planning is making them crazy.
Duckie reports that Booth was shot from 20 feet away. His fingertips had chemical burns.
Bank records show Booth's records were all cashed out and put in a trust for his wife. He filed a police report a week ago saying someone tried to run him off the road.
The morning he died he called Westfal, his wife and an unlisted number. McGee traces it to Penelope Langston and freaks out. He runs out of the office.
Tony and McGee and go meet Penelope (Lily Tomlin), his grandmother. She knows Booth is dead.
Booth was a student of hers, but they stayed in touch. She says he was having trouble at work, but didn't know he was working at Telis. She knows it's a military think tank. She tells McGee not to make connections where there are none.
They leave and McGee is sure she's lying, the way she deflected reminded him of his dad. They want to figure out what she's hiding.
In the lab, Abby plays with a copy machine from Booth's basement. His fingerprints were singed by the old copier. He must have made 4,000 copies.
In the office, McGee finds that Penny never taught Booth. She retired before he started. Tony puts Andrew Pike, rival of Telis founder Max Elswood, on the big screen. He was fired in the 70s. McGee finds a bunch of emails from Westfal, including one telling Booth the Annex Principle is privileged information and he'd better come clean before things get out of control.
Gibbs and McGee go to talk with Westfal about the Annex Principle, which is highly classified. Westfal says Booth was stealing files -- close to 4,000 pages of privileged documents. He admitted he gave them to a woman who was a "close friend." Max looks at the wall and sees a picture of his grandmother with Telis founder Max Elswood.
McGee goes to talk to Penny, who says she made a promise to Paul that she'd keep his family safe. She says she can't tell him. She walks away from him in a parking lot and is nearly run over by a car. McGee pulls her out of the way before she's hit.
Back at the office, McGee's trying to track down the car, which was a rental. McGee tells Gibbs that once Penny is committed to a cause, there's no swaying her.
Tony gets a call from a reporter named Michael, asking about Booth's murder and mentioning the Annex Principle. He says he's been meeting with Penny about it.
Gibbs talks to Penny, who still won't talk. Gibbs accuses her of knowing about the murder and McGee interrupts. Gibbs takes him out into the hall and tells him they need to know what's going on.
McGee goes to talk to her alone. He knows she worked as an analyst for the Telis group, then quit. She published a paper and Max Elswood asked her to work on the Annex Principle in 1968. She says they lied to her, that she was creating a weapon.
She says they were about to go to print when the Vietnam War ended and they thought the Annex Principle was shelved.
Booth learned she was one of the last living members of the original group. They were trying to finish what she started.
McGee tells her how much she means to him.
The team talks to Andrew Pike in MTAC. He's in Bali. Penny told them Andrew threatened to make Telis pay for stealing his idea. Elswood wanted to market the Annex Principle, but Andrew left 39 years ago. He says the project is a threat to their way of life. McGee hacks into Telis' secret files and searches old files for the Anax Principle. He pulls up footage of a caterpillar. It was a hybrid bug and robot, a genetically engineered plague.
Penny and McGee go to meet Michael in a parking garage. She walks toward a parked car with the files, but no one gets out. The car speeds off and they see the reporter lying dead on the ground.
Back at the office, they think the killer is after Penny. McGee pulls up the original Anax group and finds it included Westfal. Penny says Westfal was power hungry.
They find Westfal signed for the rental car that tried to run Penny over.
Gibbs talks to Westfal, who says it's a forgery. He says he admired Booth for the risks he took.
In the lab, Abby reports they found a super strong carbon fiber on the victims. She traced it to a Vietnam-era gun used by the Army.
McGee finds Ellswood and another guy served in the Army, but the other guy is way too young to have used the gun. Ellswood supposedly died in a plane crash 20 years ago, but his body wasn't found.
McGee checks on Penny but finds she left.
Cut to Penny trimming her bonsai tree and hearing a rustling. A man in a fedora and sunglasses steps out. It's Max.
He accuses Penny of trying to destroy his legacy. He has a gun. But Gibbs and the team are there before he can draw it.
Back at the office, Penny tells embarrassing McGee stories.
She primps for her ride home. She says Gibbs reminds her of his dad; he loves McGee but doesn't know how to show it. She urges him to take the first step and call him. He says it's been seven years.
Penny's ride home arrives, cocktails with Duckie.
She urges McGee to call his dad. She and Duckie leave. McGee picks up the phone and calls his dad.