This episode bore some parallels to Pauley Perrette's real life. She divorced her ex-husband, Coyote Shivers, and took out a restraining order against him, a restraining order he violated and was arrested for.
When Gibbs walks in to MTAC to brief the director, he finds her coordinating an operation on a Turkish ship. That operation is fully revealed in the two part episode Hiatus (Part I) (2006) and Hiatus (Part II) (2006).
The first scene in the Autopsy room, when Ducky is suggesting to Jimmy the order in which to identify and put together the pieces, the technical phrases he uses are a medical form of the the words to the song or hymn "Dem Bones" or "Dry Bones": the toe bone's connected to the foot bone...
Mimi Kuzyk, who played Ginger Stevenson, once played NCIS: New Orleans (2014)'s Scott Bakula's wife on Quantum Leap (1989), another Donald P. Bellisario show.
When Ziva reports her suspects to Gibbs, she hands him a folder he glances at, then informs him "Unfortunately they both have airtight alibis." He immediately tosses the folder blindly behind him.