Lt. Johnson falls to his death during a training exercise when his D-Link snaps open. Since his team was training for a secret mission, most information is classified. Abby finds someone's partial fingerprints on the D-Link and also discovers that the faulty D-Link was handmade from an aluminum which is weaker then the factory manufactured ones that are made from steel. She assumes that someone substituted Lt. Johnson's link to cause a murder.
NCIS now has 38 hours to find out what happened exactly or the mission would be cancelled. All special team members had no contact with the outside world except Petty Officer Vengal who called his pregnant wife two weeks ago and was written up for the unauthorized absence. Vengal says he had to take his wife to the doctor. Abby finds a match on the D-Link in the criminal database – it's Mrs. Johnson's.
Johnson's widow says the criminal record is for a car theft when she was 16 and it was her boyfriend who stole the car. As for the fingerprint, she was just picking up the stuff her husband was leaving around. Tony asks if her husband was sleeping in the den and she says they were having problems. NCIS confiscates their laptop. From Johnson's notes, they find out that Vengal lied as he took his wife to a doctor an a different day and also he was not recommended for a promotion.
When Kate checks Johnson's phone records, she finds out he called Father Clannon, his best friend, however, Father Clannon can't talk to NCIS about things said during the confession. In the evidence room, the cell phone is vibrating as it receives a text message from an e-mail account asking Lt. Johnson why he wasn't there. Abby and McGee start hacking the servers while talking about their relationship.
PO Vengal is brought in to be interrogated. It's revealed that he was late to the squad meeting and was written up but he lied about taking his wife to a doctor because he went to an off-base doctor himself for the inner ear infection so he wouldn't be taken off the mission. He had no reason to kill Johnson as it would get the mission cancelled and Vengal put everything on the line to go on that mission.
Now the team has to start from scratch. Kate wants to know how rapelling works so she would have a better understanding of the case. When she tries it out, she realizes that the faulty D-Link was lighter than the regular one and such an experienced climber as Lt. Johnson would've noticed the difference.
With less than an hour left for the mission to start, NCIS finds equipment in Lt. Johnson's garage where the D-Link was made and Abby finds love letters on Johnson's secret e-mail account. Mrs. Johnson says she suspected something a couple of years ago, and about two weeks ago, followed her husband when he told her he was going hunting.
She tracked him to Baltimore where he spent two days in the hotel and when he came outside, she saw him hug a man. She didn't tell this to NCIS because she didn't want to embarrass Lt. Johnson and hoped his death had no connection to it and now she blames herself for confronting her husband. Gibbs tells the CIA that Lt. Johnson's death was a suicide.