US Special Forces capture Mustafa Atef, who is believed to be a very high ranking Al-Queda official instrumental in training the hijackers who attacked the World Trade Center & the Pentagon. As a result, the President convenes the first military tribunal in over 50 years. As none of the JAG staff is eager to defend the accused terrorist, Adm. Chegwidden takes it upon himself to defend him, with Cmdr. Turner volunteering to sit second-chair for the Admiral. Harm & Mac are assigned to prosecute.

The tribunal is held aboard the USS Seahawk, so with the senior JAG staff flying out to the carrier, Lt. Singer is placed in charge of JAG's Administration Staff, much to the dismay of Harriet and the others. Lt. Singer then takes over the Admiral's office, conducting a fire drill and generally making a nuisance of herself.

On board the carrier, the staff are reunited with Bud, who as fleet JAG is assigned to assist Harm & Mac.

Admiral Chegwidden, Lt. Singer & Cmdr. Turner move over to the Pentagon War Room to easily coordinate & share intelligence information on Kabir Atef's planned attack on the U.S.

When an Afghan school is destroyed in a bombing raid, Bud & PO2 Coates fly to the scene to survey the damage. Once there, he promises to the locals that the US will re-build the school.

Meanwhile, Harm & Mac are still in Afghanistan attempting to pick up Kabir's trail, still looking for the mysterious truck that disappeared during a raid. ("In Country"). They come under fire, but are unhurt. Once they repair the damage to the vehicle caused by the gunfire, they continue driving all night and find an abandoned truck that appears to be the one they're looking for. They find the driver dead of suspected origin. Continuing onto the next village, they find villagers in the same condition. A medical team is brought in and they determine that the villagers are suffering from radiation poisoning.

The episode starts with a short recap of where we left off last season: Bud & PO Coates walking along a dirt road enroute to attend the ground-breaking of the new school, when they spot a small boy playing in a field that had yet to be cleared of mines. As Coates runs for help, there is an explosion behind her. She turns in time to see Bud injured in the explosion and runs to his side. Coates insists that Bud must be transported on the helo that brought them in, that Bud won't be able to wait for the proper medevac chopper.

Bud is airlifted to a field hospital, critical, but still alive. As luck would have it, ZNN reporter Stuart Dunston just happens to be at the base camp when Bud is brought it. Dunston reports the arrival of an injured JAG officer that was brought it, but does not report the name. Chegwiggen advises Harriet, but reminds her he is still on the Seahawk. She tries to contact him by instant messaging, but does not receive a reply.

Harm and Lt. Cmdr. Manetti travel to Naples, Italy when an Interpol officer believes someone aboard a US destroyer is a serial killer who has killed four women while on leave in European ports.

Mac remains onboard the USS Seahawk until a replacement for Lt. Singer is assigned. (See ""Notes"" below)