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An alien craft's appearance near a cargo freighter in the Atlantic Ocean seems linked to the deaths of most of the crew. Dr. Molly Caffrey, a government contingency analyst, is called in to investigate, and she assembles a team that includes a NASA microbiologist, a physicist, a covert operative, and an expert in languages and mathematics to probe the mystery.

Gunneson attacks Molly in her home, but he escapes and the Threshold team tracks him to a water-treatment plant, where they encounter another infected person. And Molly fears she may be more affected by the alien signal than she first thought when her blood congeals into the fractal alien pattern.

Molly and her team fear that cadets at a local military academy have been infected by the aliens after a janitor at the school viciously attacks several people before his head implodes. The investigation leads Molly to suspect that an infected cadet may be attempting to send an alien signal across the Internet that could affect millions of people.

An inmate at an Ohio psychiatric institute escapes and Molly believes he may have been infected by the aliens after paintings of glass trees, like the ones in her dreams, are found in his cell. The inmate, who has been incarcerated since 1979 for burning down his house with his family inside when he was 13, then breaks into a woman's ground-floor apartment and starts digging through the floor for a mysterious object he buried 26 years ago.

Park, one of the infected crewmen from the Big Horn, kills a detective at a Baltimore port during a shoot-out with an Asian gang that is smuggling highly sophisticated computer microchips. When Molly arrives on the scene, she learns that Park survived being shot at the docks and electrocuted on a nearby fence while he was trying to escape. But what she learns next worries her the most: human technology can create the deadly alien signal.

Molly and her crew descend on Miami after partygoers there are exposed to the alien signal and begin bleeding and fighting one another. The Threshold team quickly learn that the signal came through a dance-mix recording that was played by the party's female deejay, who is being taken over by the aliens. As the team searches for the missing young woman, they try to trace the signal's origin and fear that it now may be spreading through technology.

While a security leak threatens to put the Threshold plan in jeopardy, Molly fears that residents in a small Rhode Island town may have been infected by the alien signal after several people reported having disturbing dreams about trees made of glass. The leak is brought to Molly's attention when a newspaper article appears that vaguely mentions Threshold. Unfortunately, the article gets a meddling senator's attention and he insists on being included in the project.

Molly travels to Indiana after a Threshold agent who was watching the boyhood home of an infected Big Horn crewman disappears. While she's there Molly learns that one of the town's ministers may be infected. The pastor claims to have seen visions of a glass sea and is warning his congregation to prepare for the end of the world. Back in Washington, D.C., Baylock leads an effort to locate the sunken Big Horn and raise it to the surface for study.

Three women in the D.C. area come to the attention of Molly and her team when an artist beheads her husband, an oil billionaire's wife attacks a bank teller, and an attorney mutates and explodes on a street corner. The investigations reveal that all three were infected by the alien signal from a startling and unsettling source. In other events, Molly meets with the new national security advisor, who will oversee the Threshold project.