The Taelon Companions arrived on Earth a few years ago, and have cured hunger and disease. Da'an tries to enlist police captain William Boone as an aide, and so do the human underground resistance, who are suspicious of the Taelon's motives. Boone initially refuses Da'an, but then agrees (after what must be the shortest job interview ever), because his wife has died -- she was murdered by a car bomb made to look like an accident [we do not yet know who by, although we are supposed to think it is on the orders of Da'an, or maybe his other human implant Sandoval]. Boone is implanted with a CVI -- an alien virus that increases his intelligence, modified by the resistance to be without the motivational imperative to be loyal to the Taelons.
Boone, using his newly acquired cognitive abilities, sets out to discover who killed his wife. The resistance try to dissuade him -- his motivational imperative should make him incapable of revenge, suitable only for serving the Companions. Then Da'an asks him why he is doing this. Boone asks if Da'an ordered the killing to make his service to the Companions easier; Da'an denies giving any such order. So Boone pretends he thinks the bomb was meant for Da'an, thereby threatening the Companions. Da'an gives him the go-ahead to continue his search. Boone goes to Augur, a computer hacker, to find other cases. Augur eventually tracks down the killer, who is shot by the Companion's other implant, Sandoval. Sandoval ordered Boone's wife's death because he had had to put his own wife into an Institution in order to serve the Companions better. "No-one should have to suffer what I did." Boone maintains his cover and refrains from killing him (and so the resistance doesn't have to kill Boone, either). And we see Companions in their natural blue state, making conference calls.
Boone, while guarding Da'an, encounters a long-lost love, ??? Chapel, expert on a Taelon musical instrument. Their relationship soon rekindles, but then she confesses to Boone that she intends fighting the Companions. Meanwhile, a plutonium shipment has been stolen, an incident requiring his undivided attention. Boone is torn -- should he tell his love of his own double life with the resistance? But Lili is suspicious of the way Boone is acting out of character, given the recent death of his wife, and asks Augur to investigate. Augur discovers that the musician is an FBI agent working for the Companions -- and then Boone uses his enhanced memory to discover that all his memories of her are false. They were implanted by his virus, and this incident was a "quality test" of how well his motivational imperative of loyalty to the Companions had taken.
A serial killer undergoing experimental drug therapy escapes from jail, after painting Taelon script on his cell wall in his own blood. Boone is sent to capture him, because Da'an wants to question him. It transpires that the experimental drug is the Taelon virus itself, with the moral imperative "to love humanity", but that it is burning out after two years. The killer appears to have tapped into the virus somehow to discover a Taelon legend, and he thinks that he is one mythical twin who must kill the other, "the liar": Da'an. The killer captures Doctor Bellman and forces her to remove Sandoval's skrill, with which he intends to kill Da'an. Boone manages to stop him, but the killer realises Boone is also "free", and passes on his mission to kill the liar to Boone, just before he dies.
William Boone stops a young woman from comitting suicide. Peyton is a well-known car accident victim, who lost both her hands when she was ten. The Companions decide to use her as the first public recipient of their on-going, but not always successful, limb regeneration programme treatment. At first, all goes well, and Peyton identifies Da'an as a messenger from God when she sees a halo around the Taelon's head. The Church of the Companions wants her to spread the word about her gift. But then the regeneration begins to fail, and the Companions want to hide the evidence. But Boone rescues Peyton, without blowing his cover. It turns out the head of the Church is closer to Da'an than it appears.
The Taelons have ordered the destruction of the alpha strain of the skrill -- because its instinct for self-preservation is insufficiently bred out. But the mother of the line attaches itself to the human scientist who has bred them -- he has no CVI, so the skrill is in control. Boone is appalled to learn that the skrill are sentient. There is also a hint that the Taelon's first encounter with a sentient race did not go well. The resistance want to capture the skrill and study it. Boone eventually manages to save the scientist, even though Da'an had ordered the use of nerve gas (knowing Boone would die, too).
A Harvard-educated Amish doctor comes to Boone for help -- members of his community are committing suicide, and he thinks it might be CAS -- Companion A??? Syndrome. Boone and Lili go to investigate, with Da'an's blessing, but the doctor is shunned for bringing in "the English". Boone and Lili eventually discover an alien artefact in the forest, that is using robot butterflies to get people to commit suicide in bizarre ways. They assume it is a Taelon device to examine human physical limits. Boone disables it after the butterflies swarm Lili in her shuttle. All ends well, and the shunning sentence is reversed.
Jonathan Doors interrupts the World Bowl coverage to announce his resistance to the Taelons. This causes a crisis amongst the Companion Synod -- with the temporary removal of Da'an. Doors' second attack -- exposure of a Taelon genetic experimentation facility -- seems to backfire because the Taelons managed a cover-up. Then Boone launches a sting operation aimed at reinstating Da'an whilst proving that Doors' allegations were right all along. We learn that the Synod is experimenting with getting human cooperation, rather than using their usual technique of enslaving the alien race. Finally, we discover Doors' secret underground base, including the alien artefact from the forest.
Because the Taelons have already given Earth all the data about Mars they would have discovered, the US Government cancels the popular manned Mars mission, much to the fury of Captain Chandler and his crew. Da'an offers them a place on the Taelon shuttle pilot program, but Chandler angrily declines, (correctly) believing the Companions are trying to keep humanity out of space. Chandler makes contact with his old pilot-friend -- Lili. She shows him her Taelon shuttle, which he proceeds to steal, to try for Mars. Da'an fails to persuade the Synod to explain to Earth why we should not go into space. Lily, Boone and Augur discover the hiding crew, and help them overcome the navigational limiter so that the shuttle can leave the atmosphere. They make it to Mars -- and also report on what they found on the back of the moon -- what appears to be a huge Taelon colony.
A group of soldiers kidnap Da'an during an astronomical presentation about the Taelon homeworld. The Major leading the group wants five of his men returned -- the Taelons had claimed to be training them, but one escaped, no longer quite human, and the rest have disappeared. However, Da'an doesn't know, or isn't saying, and the Taelon Synod refuses to negotiate. Sandoval is distraught at the thought Da'an will die. Fearing a human backlash if Da'an does die, Doors tells Boone to find Da'an fast. Boone does, but is captured by the soldiers. Meanwhile, Da'an, realising the Synod is not negotiating, submits to their wishes, and starts to die. Doors convinces the soldiers to give up Da'an, and in return he will help them find their comrades. Boone calls Da'an back from the edge of death.
Sandoval's implant begins to deteriorate, and has to be destroyed. Before he can be reimplanted, and now without his motivational imperative, he escapes, and rescues his wife from the institution where he had put her. The Synod and Da'an are running scared, and instruct Boone to kill Sandoval, because he has some extra information about the Taelons that later implants haven't got, explaining the urgency of the Taelon mission. Sandoval finds Doors, to get his wife to sanctuary. He collapses, and it becomes clear that the only way to save him is to reimplant him. While he is still human, Boone re-establishes his cover by convincing him that his wife is now dead: "I did for you what you once did for me". Once restored, Sandoval tells Boone that all he can remember of the extra information is that the survival of both species is dependent on the survival of the other -- if we destroy the Taelons, we destroy ourselves.
Doors has a crew investigating the "scarecrow" -- the alien probe Boone and Lili discovered in the Amish village -- and are trying to communicate with it. To this end Boone persuades Da'an to teach him the Taelon language. Unbeknown to them, the probe has replicated Rayna, one of the scientists examining it. The probe sends out a communication, which is detected by NASA, who ask Da'an if it was a Taelon signal. The discovery of the probe sends the Synod into a flurry of activity, to shut it down. This puts Doors' hideout at risk of discovery. The replicated Rayna blows up Doors' power source and isolates the probe, as Sandoval and Da'an close in. But Boone manages to lure the probe into a corridor, where Da'an shuts it down. [All the humans seem convinced the probe is simply a Taelon device, despite the panicky response of the Companions, and despite the fact the transmission was aimed at another part of the galaxy all together.]
An ancient mural depicting a Taelon visitor is discovered in an Irish burial chamber. The Synod is in a flap -- this is the original visitor who 2000 years ago initially advised the Taelons not to visit Earth -- they now want the results of the rest of his studies to see if they should leave. And Doors wants the results for his own purposes. Da'an hints to Boone and Sandoval that the reason the Taelons need humans is because the Taelons have made a developmental mistake that humans haven't. Sandoval teams up with the United Kingdom Companion's implant, Siobhan, to look for the actual tomb [taken with the reference that Ireland has recently been Unified, this is a politically confusing scene]. Lili and Boone do their own investigation, which requires Boone to take part in a drinking contest, and they discover the tomb first. The ancient Taelon destroyed all the research results, but left a recording pleading with any future Taelons to treat humans "as equals". Sandoval discovers them before they can hide the recording, and passes it on to the Synod. The Taelons decide that their destiny is inextricably linked with humans', and so will stay.
Against Boone's advice, Doors has Augur develop a computer virus capable of infiltrating Taelon security. Lili uses her shuttle interface to insert the virus into the Taelon Washington building. But it runs amok, infecting the shuttle too, and then all the other Taelon facilities, threatening world-wide chaos. The shuttle is infected while Lily is flying Da'an to a meeting, and it crashes, stranding them in a forest. Lili is trapped and badly injured, but Da'an refuses to leave her. The Companion frees her from the wreckage, protects her when the shuttle explodes, tends her wounds, then helps her flee from Liberation troops sent by Doors. (Lili knows she is safe, but wants to protect Da'an.) Meanwhile, Boone and Sandoval, trapped inside the shut down but still living Washington building, are desperately trying to eradicate the virus. They fail. The troops eventually catch Da'an and Lili -- Da'an, not knowing that Lili is really on their side, tries to protect her from them. The troops tend to Lili, and demand to know from Da'an why the Taelons are really on Earth. Da'an calmly tells them it is not in their best interest to know. The computer virus is now totally out of control, and threatening to cause catastrophe -- when a huge Taelon ship appears, and destroys it. Da'an asks the troops to consider the fact that the Taelons have such power, but use it only to save humanity. Lili and Da'an are brought closer by their shared danger, and they move their relationship "to a higher level", in a hand-touching ceremony, which allows her to experience Da'an's feelings and emotions. [It isn't made clear if Da'an also experiences hers; presumably she is not capable of concentrating all of her energy "in a single place in her body" in the way Da'an does. As there is a real danger her cover might be blown, why does she agree?] She will now find it difficult to be so single-minded in her work for the Liberation.
Boone starts hearing telepathic messages from Johnson, one of the soldiers who kidnapped Da'an -- but Johnson was reported to have been killed during the rescue. It turns out the Synod have kept him alive, and are about to implant some of his brain cells in the Taelon scientist Rho-ha -- they believe that de-evolution is a survival necessity for their species. The process awakens a vestigial destructive organ (which has the same name as the Taelon evil mythical twin ) in the hands. The Taelon subject de-evolves a bit too far, experiencing disconnection from the Synod, linked only to Johnson and his rage. Boone asks if this Taelon might kill another one. "No Taelon has killed another since the founding of the Synod, back in the forgotten past." Rho-ha escapes, and goes to the hospital where Johnson is in a coma. Johnson's CO surprises Rho-ha, and is killed by the Taelon's glowing hands, witnessed by Lili. Rho-ha escapes again, and goes after Johnson's family. Boone and Lily go to stop Rho-ha -- the Taelon nearly kills Lili, and then takes Johnson's wife and son into the woods. Boone follows, and blasts Rho-ha with his skrill. But the Taelon recovers, and has Boone pinned down, and is about to kill him. Back in the hospital, Da'an realises that Johnson must die, to break the link. Neither Dr Belman nor Da'an can bring themselves to kill -- but Da'an gives Johnson the means to suicide. The link broken, Boone escapes, and the rogue Taelon is captured. The experiment has failed, and the Synod is contemplating killing the dangerous de-evolved Taelon -- Da'an notes that Rho-ha's violence has already affected them.
The Synod's psychic link is invaded by a human telepath, to their great consternation. Sandoval is ordered to kill her, and recruits Boone's wife's murderer to do the job with a virus tailored specifically to her DNA. Before she dies, she links with Boone, transferring her knowledge of the Taelons to him. The psychic abilities were given to the humans 2000 years ago by the ancient Taelon visitor -- in order to make the Taelons take humans seriously.
A Taelon IT weapon is stolen, apparently by criminals, but actually by an undercover Taelon operative trying to flush out Jonathan Doors. Da'an insists Lili not work on the case -- ostensibly because her estranged father has died and she must be allowed to grieve. But the real reason is that the Taelon agent is in fact her father -- who was transplanted into the body of a dead criminal after he himself had died. Lili investigates anyway, by way of Auger, and finds the thieves, but is captured by them. The real thieves want to kill her, but of course her father cannot. He tells her who he is, and they have a heart to heart. Meanwhile Boone and Sandoval are told of the ploy. Doors meets the thieves to buy the weapon, but is warned by Boone it is a trap. A gunfight breaks out, and Doors shoots Lili's father, who dies in her arms, reconciled.
The Taelon scientist Rho-ha stands trial for murder of Johnson's CO . The Taelon Synod is desperate that Rho-ha be found guilty, and sentenced to death, both to send a message to the humans, and to rid themselves of the inconvenient Rho-ha. They assign Sandoval and Boone as defence council. The DA is Jonathan Doors' estranged son, who wants to the Taelon found guilty to demonstrate that no-one is above the law. The single Taelon on the jury convinces the human jurors -- who were willing to accept Boone's argument of self-defence -- that Rho-ha is guilty, because he was not in any danger from the Major. So Rho-ha is found guilty, and the jury recommend the death penalty. But Boone does a better job than the Synod expected, and successfully pleads for the judge not to impose the death sentence. A Taelon-obsessed human becomes a walking bomb and tries to kill the DA -- but kills only himself and a bodyguard. The Taelons ask to have Rho-ha back for "preparation" -- but then they discorporate their rogue Compantion.
Taelon interdimensional travel is introduced for human use between cities. But an incident makes it clear that some human travellers are being abducted and used as guinea pigs in Taelon experiments. A deaf boy gets his hearing restored. Boone's sister becomes pregnant, but a DNA test shows the child is not hers. A member of the resistance manages to get abducted without losing awareness, and finds himself on a a Taelon facility in Earth orbit. Boone manages to rescue him before the Taelons can eliminate him. Boone's sister loses her child.
The alien probe unleashes a devastating infection on Earth, which threatens to wipe out both the human and Taelon races. Ne'eg, the first infected, dies. The Taelons are reluctant to involve the humans in research for a cure. A group of white supremacists (who claim support for their case because the clearly superior Taelons are white) steal the bug and introduce it into the drinking water of a community project. This unleashes the bug in its full fury, and even Boone gets infected. Dr Belman manages to manufacture antibodies from Boone in the nick of time -- saving humanity and the Taelons. Boone's antibodies seem to have an effect on the Taelons (one's face morphs to Boone's and back). Doors gets hold a variant of the virus that affects Taelons but not humans.
A digital Rayna, who's DNA sequence was stored in the alien probe [recreation of which appears to restore all her memories, too], reappears through the comms network to warn Augur that the Taelons have nearly decoded the probe's secrets, and will soon find out all about the Resistance. So the team, aided by a mercenary, launch an attack on the probe's base, to destroy it first. Meanwhile, Jonathan Doors' son, newly appointed as official contact between Earth and the Taelons, is badgering the head of the Synod for more information about the virus. Rayna gets recreated before the probe is destroyed, but Rayna's lover dies during the rescue. Sandoval is instructed to eliminate Doors' son, and contacts the mercenary.
Ha'gel, an ancient Taelon murderer, is discovered incarcerated under the sea by a salvage team deep, but escapes. Ha'gel can take on the form of a subject, leaving the original encased in a cocoon until the moment the murderer takes on another's form. Da'an tells Boone that, 10 million years ago, another race genetically infected the Taelons and conquered them. Later we learn that it was the Taelons who destroyed the race that saved them, and that their mission on Earth, if successful, will result in the destruction of humanity. The Companions' implants rush to find the murderer. Siobhan, the Irish implant , suspicious that Marquet does not want to become an implant herself, investigates her, intuits that she is a member of the Resistance, and tricks her into revealing the Resistance's church base. In the final battle in the church, Ha'gel, who seems to have mated with Siobhan, takes on the form of Sandoval, but is destroyed by Boone, who himself is critically injured. Boone ends up floating in a recovery tank, but a Taelon destroys him...