Delilah uncovers some intel about a murdered Navy officer, named Kit Jones. When her boss finds out, she orders Delilah to forget she saw it. Then she wipes her computer to remove the discovered data.
This doesn't sit well with Delilah so she goes to Tony and Gibbs, asking them to move the investigation forward. They agree, and pretty soon the CIA gets involved, confirming that Jones is alive and working on a bigger case for them, undercover, and that the explosion that caused his "death" was a cover-up.
It turns out that Jones was actually not working undercover at all. Instead, he was being held captive by CIA rogue officer JIm Brisco. Brisco tortured Jones for his security codes, in order to access intelligence that he would sell to a dark net site called Phoenician Exchange (PX).
NCIS took Brisco's accomplice into custody and worked out a plea deal by having her wear a wire to a meeting with Brisco. After Jones hits him with a haymaker, Gibbs arrests Brisco.
Meanwhile, Tim and Delilah had a discussion about their relationship. Tim had planned to ask her to move in with him, but her news was at odds with his: she wanted to apply for a senior analyst opening in Dubai. They agree to maintain their relationship by long distance.