The body of a Navy Lieutenant JAG officer is found in the woods by a boy scout, and random tests later confirm that the JAG officer was pregnant. Admiral Chegwidden informs members of JAG of the news when it's revealed that the body is that of Lt. Loren Singer.
Called in to investigate the body, NCIS then launches an investigation into Singer's murder. Commander Rabb calls his half brother Sergei to inform him of Loren's murder. The episode is mainly dedicated to the investigation into Singer's murder, and finding a suspect. NCIS interviews several members of JAG, including Mac, Roberts, and Manetti.
After interrogating Rabb, Special Agent Leroy Jethro Gibbs reads him his rights, and places him under arrest for the murder of Lt. Loren Singer with Special Agent Tony DiNozzo and Viv Blackadder aiding him. This is where the first part of this two-part episode ends with the storyline later picking up in the second episode, "Meltdown".
On the side, NCIS is attempting to apprehend the terrorist responsible for the attack against the USS Cole and they interrogate another terrorist, Amad Bin Atwa, who helped finance the attack. Director Thomas Morrow wants Gibbs to take over the interrogation of Atwa so as to prevent another terrorist attack against a Navy ship.