A British prison guard is found dead in a shipping container. Turns out she was taken hostage by two prisoners three weeks ago. All three were stowaways on a ship to the U.S.
The two prisoners are Cassio Chavez, a murderer, and a former MI6 officer named Jacob Scott. Scott was convicted of espionage in 2002.
NCIS is tasked to solve the murder and catch the escaped convicts, as a result of Fornell attempting to manipulate the agency into taking it off of FBI hands. Unfortunately for Fornell, his boss and Vance agrees that the two agencies - NCIS and the FBI - must join forces for the case. NCIS is taking the lead.
Homeland Senior Division Chief Tom Morrow shows up at NCIS in response to Vance's request to do so. He was the NCIS director when Scott was first caught.
Bishop suspects that Chavez's father, who works on the docks, helped his son with his escape.
Following a lead on a woman named Miranda who visited Jacob Scott in prison, Fornell and Gibbs go to her workplace, only to find her murdered, along with the janitor. Both Scott's and Chavez's fingerprints are found at the crime scene.
It turns out the convicts were after guns and money, both of which Miranda kept on hand at her workplace.
Miranda was also a former MI6 agent.
Ducky informs Gibbs and Fornell that the prison guard died from an untreated asthma attack.
The guard's death was not a murder: Abby determines that she was in the shipping container by choice, and was likely an accomplice to the convicts' escape.
Vance is on the phone when he suddenly loses the cell signal. Jacob Scott jumps into his car, and points a gun at him. Vance presses his panic button, but it doesn't send a signal. Scott is using a cell phone jammer.
Scott kidnaps Vance, warning him by telling him his children are in danger if he doesn't comply.
Gibbs and Fornell are in MTAC, talking with Morrow and the British Prison Service Custodial Manager Chester Grimm. Suddenly, the comm goes down as the system resets itself. A result of an attempted intrusion.
The intrusion is caused by Scott attempting to access NCIS records using a special SOS NCIS password, which is only used when the user is under duress. That pass code is retained by Vance.
Gibbs, McGee and Fornell rush to the building where Vance's code was used. They find him locked In one of the rooms.
It turns out Scott only escaped with a single page of unclassified information. The page contains the names of six NCIS operatives involved in a joint MI6 operation in 2002, call Juniper Strike.
Abby discovers the home that the prison guard set up for herself in the U.S. Tony and McGee realize that's probably where the two convicts are staying.
Fornell and Gibbs capture Chavez at the prison guard's house.
Chavez tells Gibbs and Fornell that he and the prison guard were planning to be together as a family.
Chavez confesses to killing Miranda and the janitor.
He tells them Scott is out to kill Gibbs. He blames Gibbs for the death of his wife.
It turns out that the Russian to whom Scott was giving secrets (and who was killed in Juniper Strike) was secretly married to him. The list he managed to get using Vance's credentials contains the names of all the NCIS agents involved in the Russian's death.
The list of NCIS agents: Janet Ashford, Kevin Dresser, Lucas Green, Allen Kane, Kyle Reed and Emma Shaw. Former NCIS director Tom Morrow's name is on the page as well.
The team rushes to Morrow's house. They rush in and find him dead in his den. He was sniped.