Gibbs discovers that his former mother-in-law Joanne (Shannon's mother) is somehow involved in the murder of a Navy captain. She's found near the body, but claims that she saw a masked gunman shoot at the victim and flee. However, evidence suggests that she was facing the Captain Norton rather than having her back to him, and that she might have actually been the one who pulled the trigger.
There was some question of whether Gibbs could work on the case and still remain impartial, but it's decided that he can. The team finds out that Captain Norton had made a lot of money helping a Mexican drug cartel smuggle their goods into the US. More digging reveals that this was the same cartel which killed Shannon and Kelly, and so Joanne would have motive for dealing with Norton.
The murder weapon is owned by Lt. Shankton, who has a fishing charter business which he runs in Mexico, the perfect cover for drug-smuggling. Meanwhile, Gibbs asks M. Allison Hart to be Joanne's attorney in the case. Joanne actually confesses to the crime and is arrested by Gibbs, but since she wasn't read her Miranda rights beforehand, the confession can't be admissible in court and Joanne is released.