Dr Sloan Parker is a geneticist. When her friend and mentor Dr Ann Coulter is killed after making a discovery about convict Randall Lynch, she continues the investigation. She discovers that there is a new species of human, intent on exterminating the competition -- us.
Sloan searches for more of the new species, but only finds more things to puzzle her -- including some strange slabs, and EEGs of Lynch's hyper-active brain. Lynch escapes from prison, and nearly kills Sloan, despite police protection, but she is saved by the fake-FBI agent Tom. Attwood, the new director of the Lab, goes public with the species findings -- on the instructions of a shadowy figure.
Lynch returns to the caves with Kelly and her friend as his captives. While learning more about the new species, Sloan gains Tom's trust, but endangers his life. Sloan analyses a blood sample from Tom; it has the same antibodies as Lynch's, antibodies that could have arisen in only one place, in Mexico.
Sloan, Ed and Tom travel to Mexico, and find a strange pillar buried in the desert, and the mummy of a ten-year-old girl, a member of the new species, who has four uteruses. They calculate there are now nearly 200,000 of the new species alive. The new lab director seems to be answerable only to the head of National Security. Tom is captured and tortured by his mother, but rescued by Sloan and Detective Peterson. He has the same tattoo found on the mummy, and seen on the beds: it marks him as a leader.
The mysterious pillar is taken from Mexico, and Sloan and crew have to decipher it before the Dominants find it. Ed and Tom work on it while Sloan and Peterson try to find emigrants from the next Mexican valley. One old woman tells a story of watching the Dominants looking in a particular direction as they carved the pillar; Sloan realises that it's a star map, part of which matches Tom's tattoo. They just decipher that the extra dots mark a comet due back soon when the Dominants find them, and in the shoot-out, destroy their data.
A reporter who knows too much about the Dominants is in danger.
Sloan and Tom hold Lisa captive, but fail to get any information from her during interrogation. Attwood's shadowy government boss takes over, and allows Lisa to escape, as a ruse in order to follow her back to Lewis. But the escape is too successful: Lisa gets away, and Sloan is captured. Tom tracks down Sloan, but is then captured by Lewis. However, following some deep plan of his own, Lewis kills Lisa, and allows Tom and Sloan to leave. He then goes on TV and accuses both of them of being serial cult killers: now the police are after them both.
Meanwhile, Ed had been trying to find out what's wrong with Kelly. He discovers her DNA has been altered -- she's now 1.3% different from homo sapiens -- not quite the 1.6% of the new species -- the experiment seems to have failed. Ed desperately searches for a cure, but Kelly dies. Ed learns that her friend and co-captive has disappeared.
Tom and Sloan stop in a motel while on the run, and Tom admits to Sloan that he has killed five times. Lewis sets the police on them; Sloan is caught but Tom escapes. Sloan is bailed from jail, in the hope that Tom will try to contact her. He does, but eludes the police. Lewis phones him, and speaks a code phrase, releasing some kind of post-hypnotic compulsion. Slamming Sloan out of the way, Tom rejoins Lewis and his mother, where his mind is reprogrammed, and he is ordered to kill Sloan and the others. First as a test he is made to shoot his mother. Attwood sets a trap for Tom, and he is captured. Sloan manages to reverse his reprogramming, reawakening his conscience. He then captured Lewis.
Meanwhile, Ed is investigating Kelly's death. He spots something crawling under her skin at the wake, and performs further tests. He extracts a deer tick that seems to be responsible for the DNA change: when one of the monkeys has it injected, its DNA starts to change, and it becomes violent and kills the other monkeys in its cage.
Attwood's boss is given some information: some kind of experiment is being tried on a school full of children. Sloan and Peterson are sent to investigate. They find nothing obviously wrong, but manage to get some blood samples. When Ed analyses them, he finds nanites that are destroying the children's immune systems. It is being administered to the children in their orange juice, with the collaboration of the school Principal. Tom discovers the source of the information is a 16 year old Dominant, Shaun, working for the government. Ed calls in the help of his old professor, Ian Copeland, and discovers a way to stop the nanites. But then Shaun tells Tom that Copeland is the source of the experiment -- too late to save Ed, who is injected with something, then abducted, by Copeland.
Ed awakes to find himself in a Dominant-run medical laboratory, in an Alaskan cemetery, north of the arctic circle. Copeland tells Ed he must help his research, but Ed manages to escape. He collapses, and is taken to hospital, where he is diagnosed with flu.
Sloan and Tom question Shaun again, who tells them of an Alaskan 'holocaust' project. Attwood and Peterson search Copeland's deserted office, and print off the numbers of the last ten faxes -- two from a car rental company in Alaska. Sloan and Tom hotfoot it north. Sloan sees the grave markers -- everyone died in 1918 -- and realises the Dominants are experimenting with Spanish flu. Then she and Tom are captured.
A flu epidemic sweep the whole town, which is quarantined. Attwood arrives. Back at the cemetery lab, Copeland realises he is infected -- the virus has mutated and their vaccine is useless. He tells Sloan that she and Ed must help him develop a new one. After Copeland collapses, Sloan manages to phone the sick Ed, who talks her through the process. She succeeds, but too late for Copeland.
Attwood asks Sloan to identify a murder victim: it is Tom, and witnesses identify the dead Lynch as the murderer. Then Tom turns up unharmed in Sloan's apartment. Ed identifies the victim as a clone of Tom, and the murderer as a clone of Lynch. He is out to get Tom for his "brother's" murder. After Attwood, Sloan and Ed give a press conference about the new species, Tom and Sloan are moved to a safe house, but Lynch finds them, kills the guards and abducts Sloan. Tom finds Lynch threatening Sloan with an axe, but Tom shoots him before he can hurt her.
Tom and Sloan investigate Kevin, a very violent 9-year-old boy who has attacked three older, bigger boys. He is a member of the new species, although his mother is normal: the dominants breed true. Kevin also has the ability to cloud normals' minds, and nearly kills Sloan, twice. Attwood gives another press conference, telling the world all they know of homo dominant . Kevin escapes and joins a dominant school.
Ed is making progress on his DNA conversion therapy, successfully converting a monkey. Tom insists Ed tries it on him, much to Sloan's dismay. Ed does, and Tom becomes human. But then the monkey dies, and Tom gets very sick. He survives, but his DNA reverts. Meanwhile Attwood is setting up a meeting with the leader of a moderate dominant faction, but is betrayed by his boss. It ends up with the lab closed, Attwood on the run, and Tom captured and caged by the government.