The team is called to investigate the death of a Marine private during training and discovers he had suffered a number of wounds from repeated beatings and stabbings.
They discover that the CO's brother was tortured and killed in Iraq, and he was trying to "toughen" up his men in preparation for what they might face in battle.
Meanwhile Director Vance, still on an administrative leave of absence following the murder of his wife Jackie, discovers that she had secretly set up her own bank account and hired a lawyer to draft a Separation of Property letter.
Worried about the implications, Vance returns to NCIS, assisting in the case on an investigatory level, rather than immediately resuming his role as director.
Vance is still unsure of what to do with his life without Jackie, though Gibbs reminds him that he still has his two children to take care of, giving him a purpose.
The key point involved the fact that she started preparing around the time the NCIS building was bombed.