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The Vice-Chairman of the Joint Chiefs - Admiral Kendall - has a wayward daughter (Amanda Kendall) living in Marseilles, France. As she presents a security risk, he tasks Tony with retrieving her, under the pretext of providing an overdue seminar on internet security to the NCIS Marseilles team. Tony is instructed to keep his mission secret.
Upon arriving, Tony discovers that all of the NCIS Marseilles staff have been shot dead, and Amanda is missing. The French police, led by Inspector Cheblis shows Tony a picture of Amanda escaping the building, but he denies knowing her.
Inspector Cheblis asks for Tony's gun, so she can inspect it for residue and ensure that it has not been recently fired.
After Tony tracks Amanda to a bar, Inspector Cheblis shows up, and points Tony's gun at them. When he doesn't immediately surrender, she shoots one of her fellow officers.
As Tony and Amanda escape, the inspector issues a BOLO for Tony, framing him as the killer.
Back in D.C., the tortured body of a man is found in a septic tank near some off-base Navy housing. He had been posing as an employment officer, but in reality was a spy who knew Amanda when they were in college together.
While Tony and Amanda are on the run, she keeps trying to escape to go back to Marseilles. Tony finally confronts her and learns that she actually isn't the wayward daughter he thought she was. She had been acting as an agent of the Defense Clandestine Service, under the command of Zakaria Hassan, the man found in the septic tank. While in France, she had turned a Russian arms dealer named Amir and had convinced him to work for the U.S.
The reason she kept trying to escape back to Marseilles was that she wanted to rescue Amir.
She and Tony head back to discover him being tortured. As they rescue him, his captors turn their guns on Tony and Amanda. Just then, Interpol agents step in to rescue them, and Tony shoots one of the captors in the forehead.
In the final scene, Palmer learns that Breena is pregnant.