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A former CIA operative, Victor Potter, is blown up by his lighter on his balcony. Hetty asks her team to investigate, acts suspicious, and then disappears. Potter spent the night with two escorts the night before his death. The team tracks them down, finds one dead, and the other almost dead. She says they were hired to hang out with Potter and then play a practical joke with his lighter by Paul Ruiz. The team is then pulled off the case, but they don't let up.
When they approach Ruiz, he is killed in a drive-by shooting. They don't catch the car. When they return to the boat house, Callen convinces Nell to open Hetty's locked cage so they can look into what she was doing. They find a picture of Hetty with Potter, Granger and another guy. They identify the mystery man as Barry Brooks, who had an issue with Potter. They find Brooks dead in his home, but he left a clue in his blood and a trip wire.
Between clues that both Brooks and Hetty left, the team tracks Hetty to a CIA safe house. They go there just before it is attacked. They take out the shooters and get the truck too before it escapes for a second time. Inside is Fatima Khan, she says, then pulls a gun to shoot Callen. Hetty shoots Fatima before she can though.
Fatima was seeking revenge for the death of her father many years before. Hetty, Granger, Potter, and Brooks were involved in a taxi bombing to take out a terrorist. Fatima's father was collateral damage. Granger asks Hetty if she would do it again and she replies that two lives saved many others.