Callen is facing the fallout of shooting Janvier (the Chameleon), suspended from NCIS while the case is investigated and forced to go it alone, even though Iranian hitmen are tailing him.
Meanwhile, the rest of the NCIS team interrogates Kelvin Atley, a CIA agent accused of leaking information to Iran. He informs them that he's hidden a file with all of his encrypted information about an Iranian spy in a safety deposit box, so Deeks and Kensi are sent in to retrieve it.
The Iranian agents are also on the hunt for the file, since they believe it holds the identity of the spy in Tehran, and they secure it after a shootout in the streets with NCIS.
Based on the information in the file, the Iranian agents kidnap a still-suspended Callen and try to beat a confirmation out of him. He informs the Iranians that there never was a spy; it was all a plan by the CIA to convince Iran that one of the CIA's top Iranian targets was actually a double agent.
NCIS played along with the CIA by pretending to have Callen kill Janvier. Then, he offers a trade: his life for the life of Janvier, the man who unknowingly blackmailed Iran with false information.
The Iranians agree to the trade, Callen is released and his suspension from NCIS is lifted, and Hetty rejoins the team after her latest fake resignation.