Kensi and Deeks struggle with how to act around each other after their night together. Kensi shows up to work in the same shirt as she wore the previous day. Between that and their awkward behavior everyone on the team knows something happened. Their work performance suffers and puts their team risk.
Ron Hill is decapitated during the theft of a thumb drive holding a plan to disarm Pakistan. It's blamed on Indian Gurkas, but it was the Pakistani ISI that stole it. The drive ends up in Los Angeles and the team needs to retrieve it. A Gurka shows up to take out the ISI agents for framing them for the theft.
In the end, NCIS recovers the thumb drive, but the mission isn't without problems. Deeks and Kensi's feelings disrupt the mission and the Gurka betrayed both NCIS and his government. The job was sloppy, but they succeeded.
Kensi and Deeks decide to talk about their relationship that night. When Kensi returns to the office with Sam and Callen, Granger announces that she's been reassigned. Deeks shows up and is distraught over Kensi's absence.