While Akatsuki discuses the true goals of their organization, Naruto continues his training. Meanwhile, Tsunade receives the tragic news.

Kirsten hits rock bottom after Caleb's funeral, prompting Sandy to finally take action; Jimmy Cooper resurfaces and almost immediately renews ties with a mourning Julie; Jess bullies Trey into participating in a drug deal that turns into a shootout; Ryan finally learns the truth about what happened between Trey and Marissa, leading to a bloody confrontation.

An exasperated Grace tries to mediate between a resentful Will and her sloppy, free-spirited boyfriend Nathan when Nathan moves in while Jack is in a royal dither as he plans to finally meet his unseen father face-to-face. However, Grace grows nervous when the two polar-opposite men find some common ground and she ponders how a devoted boyfriend might affect her equally important relationship with her longtime buddy Will. After settling his father issues, Jack later gets the surprise of his life in a most unexpected fashion.

When one of their own is killed, the team must find the killer before they get to another member of the team, Gibbs. In an emotional investigation, the team tries to stay together, against the wishes of Assistant Director Vance.

The Tree Hill residents are forced to face their fears as Dan turns over on a new leaf and Brooke makes the hardest decision of her life. In the meantime, Haley's career takes a turn and Peyton is visited by somebody from her past. Lucas is still struggling to mend his heart after Lindsey left him at the alter. Mouth and Millicent meet a new face. With all, Lucas and Brooke help each other through the struggles.

Jack takes his fight directly to the President as he attempts to force a confession from him that will prove his involvement in the day's events. Martha vents her hatred for her husband in front of the press as Logan gives a eulogy over Palmer's body. Jack and Audrey share a tender moment when it seems the crisis has subsided, but Jack finds that his problems have only begun as his past catches up with him.