As NCIS mourns the loss of Ducky, the agents find comfort in working on one of his unfinished cases involving a woman whose father was dishonorably discharged from the Marines.
The NCIS, FBI and MI6 teams continue the international manhunt for an escaped British spy who's targeting current and former agents. Anthony DiNozzo bids farewell to NCIS.
Having not heard anything from Ziva, Gibbs, Tony, McGee, and Abby wonder; each starts sniffing and digging; they trace her to Somalia. Gibbs, Tony, and McGee go there; Tony and McGee become caught.
After a malnourished and confused 9-year-old is found hiding in a storage unit, the team reopens an old missing persons case that Special Agent Ziva David had a personal interest in.
While investigating an off-base burglary at an Admiral's residence, NCIS becomes involved in a case of an older man that claims to be a Pearl Harbor survivor. He wishes to have his remains buried on the USS Arizona.
Tony opens a letter, literally SWAK, dispersing a fine white powder; the gang does the drill. Kate and Tony get a free trip to Bethesda. Gibbs and company search for both the bad lady and what concerns her about a two-year-old rape case.
An ambush in an alley behind a bar leaves one Marine dead and one very ill; the gang investigate. The survivor is from Gibbs's hometown, and the team goes there; flashbacks abound. The bunch put the pieces together and nail the bad guys.
Tony returns early, in time to rejoin the team in an investigation of a shooting of two Naval aviators. Tony finds a bomb, then it explodes; Gibbs says that someone has again tried to kill the NCIS gang, which loses one of their members.