Students from the College of William and Mary face off at a bowling alley during Greek Week 1999. Eighteen-year-old Taylor Watts exits the building when it is announced that someone forgot to turn off their automobile's headlights. A classmate named Nick Carfahna follows her into the parking lot. The pair are attacked by two men, one wearing a military-style mask, and a second dressed as a security guard. As Taylor is dragged to a nearby car, her wallet falls from her purse, identifying her as Peter Watts' daughter.
Watts reviews the case for a group of FBI agents. Nick, who survived the attack, provides police with a description of a single kidnapper, whose mask resembled the type issued to troops in Kuwait. After the briefing ends, Emma tells McClaren that no mention was made of the Millennium Group or its enemies. She is also puzzled by Frank's absence. A short time later, Emma finds Frank looking for clues at the bowling alley parking lot. He believes the entire abduction was precisely planned. Meanwhile, one of the kidnappers, a man named Swan, binds Taylor's hands and ankles to a stainless steel examining table. He proceeds to remove her clothing and cleans her body using a power sprayer and coarse brush. Moments later, he photographs her using a Polaroid camera.
The investigators get a break in the case when police discover an abandoned car used in the abduction. As Frank observes the scene, he experiences internal visions of Operation Desert Storm. He also notices tire and boot prints left behind by the kidnappers, as well as the smell of spectrumaldehyde, which is used for the destruction of genetic evidence. Watts arrives at the scene. Sitting by himself, he gazes at Swan's Polaroid of his daughter.
McClaren's team determines that both the tire tread and the boot prints were formed by items purchased from a military PX. Frank helps narrows the search for a culprit when he mentions the spectrumaldehyde. The clues lead FBI agents to the home of David Couger. But when they storm Couger's house, they discover that he has been tortured and executed. Given the nature of the slaying, McClaren concludes that the second kidnapper executed Couger. But Frank suspects otherwise. He believes Couger was murdered by the Millennium Group. Meanwhile, inside the stainless steel room, Swan pulls a safety tab from a canister and sets it near Taylor.
Frank learns that Couger was once a patient in a psychiatric ward at a military medical center. One of the physicians at the center leads Frank to dozens of file folders which contain information on other patients who were part of Couger's group. Frank notices that one of the folders is empty. The folder belongs to Eric Swan. As Frank exits the medical center, he encounters Peter Watts. Watts produces another Polaroid, this one depicting a sickly-looking Taylor, her eyes jaundiced, sitting near the canister. Watts believes his daughter has only thirty-six hours to live. He pleads for Franks help.
Emma determines that Swan used to call Art Bell's radio talk show - a forum for conspiracy theorists - using the pseudonym "Thomas Paine." Bell cooperates with the FBI investigation. He hosts a program devoted to the topic of the Gulf War and soldiers who were exposed to biochemical agents. Swan calls the program and claims that while serving in the Gulf War, he received orders to fire a biological weapon at U.S. soldiers (as part of an effort to test the weapon's effectiveness on fully inoculated soldiers wearing protective gear). Swan followed orders and killed an entire platoon. The U.S. government blamed the incident on the Iraqis. Bell then introduces Frank to his listening audience. Frank describes for Swan the manner in which his own wife died. Swan recognizes the symptoms. He tells Frank that Catherine died of the Microplasma Flavivirus. Swan believes his order came not from the U.S. Army, but from a group that does what "the government can't do." Swan then pulls an antidote-filled syringe from a refrigerator.
As Swan talks, FBI agents trace the source of his phone call. But when they storm the house, they find two cell phones taped together. Emma realizes the call was forwarded, and that the signal is now lost.
Using the Internet, Emma manages to locate an e-mail address containing the pseudonym "Thomas Paine." She and Frank locate Swan's hideout, but inadvertently trip an alarm as they move up the driveway to Swan's house. Frank exits the vehicle and uses his cell phone to contact Swan. He tells him they can work together to expose the men responsible for the platoon's loss. Suddenly, a shot rings out, and a window on Swan's house explodes. Frank moves towards the source of the blast and finds Watts, Mabius and a sniper. Swan tells the men that although he possesses the antidote, he is willing to let Taylor die unless his demands are met.
Watts takes the cell phone. He gives Swan the exact coordinates of where the biological weapon was dropped, along with other information proving that it was the Millennium Group that gave the orders to fire upon U.S. soldiers. He then asks for his daughter to be released. Swan returns to the stainless steel room, only to discover that Taylor has escaped from the restraining chair and has given herself the antidote. Suddenly, Taylor appears behind Swan. Using all her remaining strength, she snaps his neck. Later, The Watts family sits down for dinner and Taylor asks her father if Swan was telling the truth about what happened during the Gulf War. He does not respond.