When Gunnery Sergeant Joseph Wilks shows up at Marine Captain David Landis' home to join him in a run to prepare for a marathon, he finds that Landis has been killed. Entering the home, he surprises the killer, who stabs him and flees.
Gibbs speaks to Ken Ashmore, who describes the assailant.
Marine Captain David Landis is the victim. The guy who found him is Gunnery Sergeant Joseph Wilks.
Abby processes fingerprints from the murder scene and finds some belonging to Qasim Naasir, an Afghani with ties to the Taliban. He has a brother who also works for the Taliban. His name is Rasheed.
Ducky's autopsy shows that Landis was being tortured prior to his death, and that the killer panicked at the unexpected arrival of the gunnery sergeant, causing him to inflict a final stab wound that caused him to bleed out quickly.
When Tony and McGee go to Wilks' house to question him, Qasim shows up - and he's captured.
Tony and McGee question Qasim, who claims to be innocent.
Bishop tells Gibbs she thinks Qasim isn't working for the Taliban but is instead hiding from them. Abby determines that the prints on the knife belong to Wilks.
Wilks shows up at NCIS HQ and tells Gibbs that Qasim is not a terrorist; that he and Landis snuck him into the country from Afghanistan.
Tony and Bishop meet NSA Agent Martinez, who gives them some intelligence regarding Rasheed. They learn that Landis was tortured in order to tell them about Qasim's location, because there's a hit on him.
Vance tells Gibbs that Marine Corporal Collins was taken hostage in Kabul by Rasheed, who says that he will kill Collins unless his brother is returned to him within 48 hours.
Vance orders Gibbs to effect the exchange, on the orders of the State Department.
Bishop and Gibbs transport Qasim to Afghanistan.
Abby identifies the type of knife used to kill Landis. McGee and Tony go through hundreds of files to identity suspects who may have owned this type of knife.
Tony realizes that Ken Ashmore, the eyewitness they interviewed is in the suspect pool. McGee and Tony bring him in for questioning, and find the murder weapon in his home.
While Gibbs and Bishop plan with the base commander to capture Rasheed, they discover that Qasim has fled the compound. He has decided to turn himself over to his brother in order to ensure no Marines are killed.
Bishop finds Qasim's vest with a bullet hole in it.
Tony and McGee locate Rasheed's hideout via satellite. Vance orders them to send the coordinates to Gibbs.
Gibbs sends Bishop to the hideout on her own, posing her as a doctor.
As Rasheed and Qasim argue, Bishop is pushed into the room, followed by a man in a robe. It turns out the man is Gibbs, as he leads a group of Marines into a raid. Rasheed is shot and killed.
As Gibbs and Bishop get ready to leave Afghanistan they tell Qasim he's coming with them - that the Secretary of the Navy has approved a special immigrant visa for him.