Jen returns from Paris; at home she finds a curious sight. All NCIS agents in Washington must take polygraph tests; Gibbs and the gang look into that. Tony and Jeanne deal with an injured pedestrian; Jeanne introduces Tony to her father.

Tony meets Jeanne's father; Tony excuses himself to move his Mustang, which explodes while the gang watch; Ducky says that the victim is not Tony. The Frog meets Jen, but she lets him leave; Gibbs and others pursue him but arrive too late.

Fornell and his Hoovers arrive in the squad bay; he tells that the Gibbs team is under investigation for the murder of the Frog. However, the Gibbs gang investigates the FBI, and they put the pieces together and explain them to the suits.

In the aftermath of Jenny's death, Assistant Director Vance searches for Franks, who escaped the diner after killing the fourth gunman. Meanwhile, Tony and Ziva try to locate the one responsible, while dealing with the fallout of failing in their assignment to protect the Director. The trail points to a former hitman called Natasha, who Jenny failed to assassinate in Paris nine years previously while on an assignment that she and Gibbs were working on together. Since Gibbs killed Natasha's lover, Natasha has returned to the U.S. seeking revenge. Natasha, who never saw it coming, is killed by Franks, after Gibbs set a trap for her at Jenny's house. Gibbs burns down the house to cover up Jenny's death, making the public believe she died of smoke inhalation. In the fallout of Jenny's funeral, newly appointed Director Vance shreds a page from his personnel file in the Director's office and terminates Ziva's liaison status (sending her back to Israel), reassigns McGee to the cyber crime division, and sends Tony to the USS Ronald Reagan. Vance then gives Gibbs personnel files for his new team members.