Cade Foster's life starts to come apart. He's sacked from his job as a security consultant, his credit cards are cancelled, his house is broken into, and he's suffering from hallucinations, about a man with a scarred face, and the number 19. His wife is seriously concerned for him. He tracks down the cop responsible for getting him fired -- who turns out to be the man in his hallucinations -- only to witness his suicide. He finds newspaper cuttings about another man, who has killed his family, claiming hallucinations. Pretending to be the cop, he visits the man in a psychiatric institution -- who tells him about the clues he has left buried at the centre of a maze, and then starts raving about aliens. Cade goes to the maze, and unearths a book of Nostradamus prophecies. His wife convinces him not to go back to their house, but to go to a motel. There she is murdered, and Cade is framed and convicted. He discovers that he is the experimental representative of one of the 117 human personality types, being studied by aliens about to invade. He is the only one of the 117 to fight back at all successfully. He escapes.
Cade goes to Crazy Eddie -- editor of the Web-zine Paranoid Times -- because of stories of human cloning. At first, Eddie thinks that Cade is crazy, with his talk of aliens, which everyone knows are just government lies to cover up the real conspiracies. But he becomes convinced when he sees dead aliens disappear into dust. One of Eddie's contributors has stolen something from a cloning lab, and the aliens want it back. They kill him, but don't find what they are looking for. Cade discovers the object, which looks like a chrome golf ball, but no-one has any idea what it is. The aliens want it back because it contains the downloaded personality of Joshua -- one of their own. They are cloning human "husks" into which they upload themselves in order to be able to pass unnoticed. [The mechanism by which these husks disappear into dust when they die is not explained.] Using the dead thief's car's GPS, Eddie tracks back the lab's location. They go there, and manage to destroy a lot of husks, but the aliens get Joshua back. Eddie decides the previously-unknown Nostradamus book of prophecies [conveniently in English] that Cade found in the maze is all about this alien invasion -- and that Cade himself is the "twice blessed man".
A physics genius has died of the bends in suspicious circumstances, and Cade goes undercover at the lab to investigate. Fortunately he's wired up to Crazy Eddie, who talks him through the maths problems. A mysterious woman, who we saw kill the physicist as he recited equations, starts to suck Cade's brain, then realises he is a fake. She goes after another member of the project instead -- it's a secret government satellite defence grid, and she's a human telepath out to destroy it, on behalf of the aliens. Colonel Grace makes Cade an offer he can't refuse: capture the telepath for her, and she'll get the murder conviction quashed. After some highly implausible antics with a "pressure chamber", Cade saves the satellites, and leaves the telepath in the custody of Colonel Grace. But the Colonel had lied, and Cade is still a wanted man.
Cade joins an abduction therapy group, and meets Evan and Nicole. The couple believe they were abducted together, but tell different stories.
Cade is recognised, and a manhunt set up. He's chased through Montana woods by various deputies -- and a US Marshall who isn't all he seems. The Marshall captures Cade, and it turns out he's Joshua, wanting the take subject 117 back to find out what made him such a powerful adversary. "You want to know what made me like this? You did." Cade turns the tables on Joshua, and captures him. He wants to give Joshua up the police, but Joshua tries to kill them. Cade attacks Joshua to save their lives, but in the confusion they assume that Cade attacked them. In a little heart-to-heart, Cade learns more about the alien plans, and that Joshua is tired of all the killing. He realises it will be difficult to give himself up without Joshua hurting the police, but then runs into a Ranger, and convinces her to help. However, just as he is going to give himself up, she turns on him -- she's an alien too, Joshua's backup. Joshua kills her, and lets Cade escape -- it looks like Cade might have an ally on the inside.
Cade and Eddie investigate the disappearance of teenager Jason whilst drag racing past mile marker 262. The incident seems to fit a Nostradamus quatrain, and there have been several other disappearances of speeding cars over at least 30 years at the same place. Despite a sudden loss of motivation on the part of Cade, with the help of Jason's ex-girlfriend and his older brother they discover a quantum pocket. They rescue Jason, and Cade electrocutes the alien that was guarding the marker.
In Maryland, a man spying on his unfaithful wife sees and photographs a UFO, and contacts the Paranoid Times. Cade goes to investigate, because the circumstances seem to fulfill one of the Nostradamus prophecies. The photographs are too indistinct to prove anything, but just as Cade is about to leave, strange things start happening, the sky grows black, and the TV broadcasts an emergency message about an alien invasion. It's the second wave! Cade and a group of locals hide out in a basement, and he explains about the aliens. But the people just bicker and fight, and some just want to surrender. Eventually, tensions get so high that one of them shoots and kills another. The skies clear, everything goes back to normal. It was just a "test". Cade is relieved to know the second wave hasn't started, but appalled at what the aliens have learned about humans during the test. The locals band together, and accuse the departed Cade of the killing.
A teenage radio ham has picked up an alien transmission. Joshua manipulates Cade into finding the boy and recovering the disc. As he does, the aliens appear, chase him, and kill him. But then, in a time loop, a wormhole appears, and a woman from the future comes through, and stops the killing. She is from a time after the Second Wave, when most of humanity is dead, the rest are slaves, and a few are resisting. [So, like Terminator and Twelve Monkeys , time travel technology is a result of civilisation's collapse?] The resistance was inspired by the discovery of Cade's journals in Cyberspace -- she has been sent to bring him back to the future, to help them. However, Cade is more interested in rescuing the teenager from the aliens -- and the aliens are using the boy as hostage to get the disc back. [The disc cannot be copied, because of some technobabble.] Joshua and Cade exchange the boy and disc. Cade accuses Joshua of setting him up -- Joshua points out that they would have discovered the disc on their own -- and this way the boy survives. Cade decides to stay in the present, and fight the second wave from here -- maybe helping prevent the time traveller's future altogether [although the wormhole does reappear on schedule to take her back].