The TARDIS passes through a region of space riddled with exotic stellar phenomena, and arrives near a sea which moves in a mysterious way; the water seems to defy gravity as it flows up and over the spires of an oceanic mountain range. Fitz falls over the cliff edge while clowning around, and the Doctor and Anji set off to find help, only to find a woman named Etienne Grace under attack from men wearing brightly coloured cloaks. When the Doctor and Anji defend her, the cloaked men retreat, unable to deal with people who don’t fit into their instructions. The Doctor is injured in the fight, and Etty helps Anji to carry him to the home she shares with her young son Braga; she does so reluctantly, however, as too many strange things have happened to her family for her to trust strangers. About a year ago, her cousin Ansac was murdered, her sister Treena’s baby was kidnapped, and Treena herself was shot during a botched bank robbery; and neither Ansac nor Treena received the Creator’s blessing before they died. The Doctor is intrigued, and not just by the tales of murder; Etty seems to take it as a matter of fact that her Creator will tell her the meaning of her life when she dies.
Fitz has fallen onto a ledge just over the cliff edge, and as a storm seems to be coming in, he has no choice but to limp along the ledge looking for a way back up. He finds a tunnel leading to a cave where a cloaked man guarding a hover-van tries to kill him; Fitz inadvertently kills him instead, in self-defense. Fitz “borrows” the cloak to keep him warm while he looks for his friends, but instead he encounters the other cloaked figures, who respond to the cloak rather than his face and assume that he is Seven, the man he killed. The cloaked people seem to have no thoughts of their own, and can only follow simple instructions coded to primary colours. Fitz is forced to accompany them back to the van, but as they return to the city they spot the Doctor and Anji returning to the cliffs to look for Fitz -- and Two, still unsure how to react to them, tries to run them over the edge. When Fitz tries to intervene, the others hold him back, and decide that he needs to go through the Wiper again. Back in the city, the cloaked zombies attend an assembly at which a man named Hox brings in an ordinary woman who has been kidnapped from the streets; she has no family or friends and will not be missed, not even by the Creator. The zombies use something like an electroshock machine to erase her mind and add her to their army, and then force Fitz into the machine for “another” treatment...
Even on this world, accidents happen. When people die before their time, without receiving the Creator’s blessing, it’s up to Diviners such as Nathaniel Dark to piece together the minute details of their lives and find out why they lived and died. However, there have recently been a string of bombings in the city; too many people are dying for no reason, and Dark is starting to lose faith in the Creator’s Design. When Dark and a working girl named Lanna barely escape a bombing by mere fluke, Dark’s doubts crystallise into a desire for action. When he sees his superior, Cleric Rammes, bawling out another Diviner for trying to reopen the Etienne Grace investigation -- which has been closed by the Holiest, the eyes and ears of the Creator -- Dark surreptitiously steals the file, seeking answers. Everyone in this society is known to the Creator, at least in theory; but the killers have never been identified, and neither has the man who was shot when Treena struggled with the lead robber for his gun...
The Doctor and Anji catch a glimpse of Fitz before the van forces them over the cliff. As they hang onto the edge, Anji hears something clink, and sees a necklace lying on a nearby ledge, pointing the way to safety. She and the Doctor return to Etty’s farm just as Dark arrives, seeking answers, and after they all share their stories, the Doctor decides to return to the city with Dark to investigate Treena’s murder and look for Fitz. He asks Etty if her other family members may be in danger, but she hasn’t spoken to them for years; she last saw Treena’s widower Derran Sherat at the funeral, and he wrote to her once afterwards, a rambling letter in which he spoke of taking her hand and walking into heaven. The Doctor suspects that Etty is hiding something, and asks Anji to stay with her and Braga. Anji helps out on the farm, but as evening falls, she hears sounds outside and sees strange marks like twisted footprints in the ground. However, Etty insists that she and Braga live here alone.
Despite himself, Dark is swept along in the flow of the Doctor’s investigation, even when the Doctor questions him about things everyone on the planet should know already. The Creator sees all, and knows how even the most casual of meetings can change a life. At death, the meaning of a person’s life is explained to them; one day, Vanishing Point will be reached when the last soul is saved. Dark is horrified when the Doctor questions him about the genetic effect of the Creator’s blessing on the human brain; the mere mention of genetics is a category-G crime, and carries the ultimate penalty. And yet, the Doctor notes that the Diviners’ mark of office is the double helix... Dark, disturbed, tries to access the files on Derran Sherat -- and is even more shocked when they are deleted before his eyes. It’s as if the fact of Sherat’s existence has been erased.
Morning breaks on Etty’s farm with the sound of hammering at the door; nobody’s there when Anji investigates, but she sees the cloaked figures approaching again, and she and Etty have time to barricade themselves in before the attack. This time, the zombies have been instructed to kill anyone who tries to stop them from taking Etty -- and this time, one of the attackers is Fitz. But at the last moment, Fitz turns on the other zombies; the Wiper didn’t work on him, possibly due to all of the things his brain has been through already, and he just played along in order to get back to the farm. With his help, Etty and Anji kill Two and drive off the others, but Fitz is separated from them and seeks shelter in one of Etty’s barns -- which opens to reveal several misshapen, deformed people, all suffering from genetic disorders and mutations. Etty tries to reassure the “mooncalves”, who are terrified by the intrusion -- all but the mature Vettul, who is delighted to see new people after so long alone, and who seems quite taken with Fitz. Anji realises that it was Vettul who warned them of the attack and dropped the necklace which saved her and the Doctor -- but as the mooncalves calm down, she and Etty realise too late that they’ve left Braga alone. The cloaked figures have kidnapped him, and although Fitz tries to stop them from getting away, the attackers shoot him in the leg and escape.
The Doctor and Dark meet Lanna at the travel shelter, and Dark, inspired, shows her a photo of Derran Sherat. She recognises him; last week, he propositioned her friend Marie, but when they got back to his flat he attacked her with a knife and she barely escaped. The Doctor and Dark go to investigate, but as they approach Sherat’s apartment it explodes, and a group of cloaked figures flee from the ruins, carrying the apparently injured Sherat with them. The Doctor puts out the fire, and discovers that it was set to destroy a man-made machine capable of genetic manipulation. And some of the parts were factory-made. To his horror, Dark finds the body of one of the Holiest in the room. He and the Doctor flee steps ahead of the police, and shelter in a cafe, to discuss what they’ve learned. The Doctor suspects that the machine was built to heal someone with a genetic disorder -- but it was built using parts which were manufactured legally. It seems that machines for scanning and manipulating genes are indeed available on this world, despite genetics being a “category G” crime... and the Doctor realises that “Cat-G” is an acronym for the four bases of DNA; cytosine, adenine, thymine and guanine. It’s more than just an in-joke nobody on this world can understand -- it’s human nomenclature, being used on a world which has never heard of Earth.
The shaken Etty tells Anji that her family occasionally gives birth to freaks like nobody else in the world. When the first of the mooncalves was born, Etty’s great-grandfather took her to the hospital -- but he and his child were charged with a category-G crime and were never heard from again. When the next mooncalf was born, Etty’s great-grandmother kept the child on the farm to raise it away from the city, but although she’d turned her back on the Creator, she received his blessing nevertheless. However, the mooncalves have never received a blessing; it’s as if they don’t exist in the Creator’s eyes. Etty gets a call from Hox, who threatens to hurt Braga if she doesn’t come to the city alone. Anji decides to accompany her and join up with the Doctor, while the injured Fitz stays behind. Etty reluctantly puts Vettul in charge, although Vettul is becoming quite wilful as she grows older, and doesn’t seem to understand the importance of rules, staying hidden, and keeping away from Fitz. Before she goes, Etty hides Two’s body in the cellar, and while doing so finds a list of numbers and letters in his pocket; Fitz realises that they’re the “names” of the other zombies in Hox’s little army.
Dark takes the Doctor to an ancillary records centre, where the Doctor builds a makeshift DNA scanner while Dark tries to enhance the image from the bank’s security cameras and try to see the reflection of the man Treena was trying to save. The Doctor theorises that the robbery was engineered by the zombies’ leader to fund his own research. While the machines do their work, the Doctor roams the centre and studies its files, while Dark belatedly reports in to Rammes. He’s horrified when Rammes informs him that the Holiest are aware that he stole the Grace file -- and have summoned him to meet them at noon tomorrow. The Doctor decides to accompany him, to demand answers of the Holiest in turn. He and Dark then study the reconstruction of the bank robbery, and realise that Treena was not trying to wrestle the gun away from the robber -- she was trying to shoot the other man. And the other man was her husband Derran Sherat. But if he was shot through the chest when Treena was killed, how could Etty have seen him at the funeral and received a letter from him later?
Hox reports certain failures and provisional successes to his master, Cauchemar. Cauchemar is dying, and needs Hox to steal more equipment, with which to build another device to stave off the inevitable for a while longer. Two-Two-E-Two is dead, and Seven-Two-C-One has rejected the mindwipe; both will need to be replaced. However, they have Braga, and Etienne will thus have to come to them. Cauchemar tells the terrified Braga that Vanishing Point is coming; the city will burn, the people will die, and the Creator itself will be destroyed. And Braga’s mother is going to help it happen. Meanwhile, Dark meets Lanna on his way home, and asks her to be with him; after all he’s learned, he doesn’t want to be alone tonight. The Doctor calls Etty’s farm to report what he has discovered, and he and Fitz share their stories. Vettul then takes the opportunity to seduce Fitz, which isn’t difficult.
As Etty and Anji approach the city, Anji realises from the way Etty avoids certain topics that Derran is Braga’s father. Etty and Derran had an affair when Treena had trouble conceiving, but as soon as Treena became pregnant Derran lost all interest in Etty, and her family shipped her off to the farm to avoid a scandal. When they arrive at the rendezvous point, Etty goes on ahead, but then the Doctor shows up to investigate; however, Etty is being watched, and Anji and the Doctor are lured into a nearby building which is then blown up around them. Anji is knocked out by falling rubble, but the Doctor carries her to safety and then sets off to find Etty -- who has found Braga’s toy bear, soaked with blood, next to a brightly coloured cloak and a note telling her to come alone next time. The police then arrive to investigate the explosion, accompanied by two of the Holiest -- who take the unconscious Anji away for study.
There are still some hours left until noon, and the Doctor thus calls up Fitz, telling him to come to the city to help rescue Anji. He and Etty then go to Dark’s home, where Dark wakes to find that Lanna has already gone quietly without saying goodbye. The Doctor sends Dark and Etty to the Diviners’ head office to steal the sacred doctrine of the Holiest, while he waits for Fitz at the hospital where the first mooncalf was classified as a cat-G; the Doctor believes that’s where the Holiest keep their own genetic analysis equipment, and thus where Anji has been taken. Meanwhile, Hox once again reports a partial failure to Cauchemar; Etty’s new friends have survived the trap set for them, and the woman has been taken for category-G analysis, meaning that the equipment Hox was supposed to steal has been called into use. Cauchemar orders him to steal it anyway, and to blow up the hospital behind him, one last horror before the concerted assault. Cauchemar is now certain, after so many mistakes, that it’s Etienne who carries the spirit of his beloved Jasmine within her; soon they will be reunited, for the last time...
Vettul insists upon accompanying Fitz, to see something of the world beyond the farm, but the Doctor is concerned for her safety; a hospital could be the most dangerous place in the world for anyone who doesn’t fit in genetically. He and Fitz disguise themselves, steal a trolley and shroud Vettul’s deformities under a blanket, disguising her as a patient; the Doctor then steals a pager, gives Fitz the number, and sends him the data store while he looks for Anji. He finds her hooked up to machines which are mapping her genome, and before freeing her, he runs a test of his own to confirm his suspicions. Ordinary human DNA consists of 97 percent “junk” with no known purpose; but according to the Doctor’s earlier analysis of Dark’s blood and the remains of the Holiest in Sherat’s apartment, Dark’s DNA consists of only 1 percent junk, and the Holiest didn’t even have that. Dark’s people have been genetically engineered, and the Doctor suspects that the 1 percent “junk” DNA is the godswitch, the gene which somehow encodes experience for the Creator’s analysis, and transmits the Creator’s blessing back. Anji has similar base pairs in her own chromosomes -- not a godswitch itself, but the potential for one. The people on this world must be related to humanity, and the presence of the mooncalves suggests that an alien presence is contaminating the gene pool. When Hox and the new Seven-Two-C-One arrive, the Doctor demands answers; he now believes that Hox takes orders from the man who used to call himself Derran Sherat, and that Sherat somehow erased his own files from the Diviners’ records. Hox refuses to answer the Doctor’s questions, and attacks...
Fitz and Vettul find Treena’s records in the hospital data store, and learn that she had been classified “cat-G” -- and that someone removed her index finger the day after her death. Fitz decides to call the Doctor, but doesn’t get a response to his page, until he happens to hear a beeping noise and follows it to the analysis rooms. Hox and Seven have gutted the analysis equipment and tied the Doctor and Anji to a bomb; Fitz and Vettul release them, but the Doctor sets off a booby-trap when he tries to defuse the bomb. He takes the detonator core with him, as he and his friends flee steps ahead of security guards who believe that they’re responsible for the bombings. Cauchemar is infuriated when he learns that the hospital still stands, and that the mysterious Doctor is stealing attention away from what should be his moment of glory.
Dark and Etty complete their half of the mission successfully, and when the Doctor studies the Holiest’s doctrine he finds that it contains the genetic coding for the godswitch. He explains to the skeptical Anji that her mental image of an omnipotent computer God isn’t accurate; the Creator’s role on this world is symbiotic. Everything in this society affects everything else, just as Anji’s genes, brain, body and mind interact to make her unique, or like the commodities markets on Earth interact in an organisation without a single central influence. Their enemy is a rogue element in this society, and his interference could bring the grand scheme of things crashing down. Bearing this in mind, the Doctor and Dark attend the meeting with the Holiest, and find the terrified Lanna already there; the Holiest picked her up as she left Dark’s flat, and she’s told them everything he told her. It isn’t Dark the Holiest were after at all; it’s the Doctor. For some time now, a blank spot has been growing in the Creator’s perception of the world, and now the Holiest think they’ve found the cause -- an outsider whom the Creator is unable to perceive. The Doctor manages to convince them that there’s someone else out there, and that only he can help them to fight an evil which the Creator cannot detect.
The Holiest release them all, and Lanna flees, terrified and determined to start a new life for herself elsewhere. This is just what most people do on this world, albeit in a different way. The Doctor’s audience with the Holiest has clarified certain things; the Holiest themselves are genetic constructs, made from the flesh of the dead to act as the eyes and ears of the Creator. According to the records in the ancillary centre, the death rate on this world is constant, but the birth rate has been dropping; within a few centuries there will be no-one left. But that’s the point. These people have been engineered to serve as carriers for the godswitch, by an alien race who discovered the genetic coding for the soul. If a person lives a worthy life, the soul passes on; if not, then the Creator re-engineers the same soul into a newborn body, giving it a chance to try again, and again, until it gets it right. Vanishing Point will be reached when all souls are saved. But Sherat has tained the gene pool; there are people on this world whom the Creator cannot perceive, and their interaction with the rest of the world is throwing the Design into confusion. The Holiest killed the first of the mooncalves because they weren’t able to comprehend how it had come to exist, but the situation has just continued to get worse. And now, thanks to the bombings and random deaths, the Design is on the point of total breakdown. Soon the Creator itself will fail, and the world will end before its time.
The Doctor wires himself up to a transmitter and takes Etty’s place at the rendezvous, wearing the cloak left for her in order to confuse the zombies sent to collect her. The zombies bring him before Derran Sherat, who is clearly dying -- and although he’s infuriated at first, he becomes intrigued when the Doctor identifies his malady as advanced cellular degeneration. At last there’s someone Sherat can talk to as an equal, and he confesses everything. His real name is Cauchemar; he was a geneticist on an Earth colony, until he committed murder in his pursuit of immortality. The ship on which he was imprisoned suffered an accident and drifted into this highly irradiated region of space, where the dying prisoners and crew were contacted by aliens who had evolved into a state of union with the Universe. This race also had its criminal elements, however, and thus they struck a deal with the humans. Cauchemar engineered the humans into carriers, living prison cells for the alien race’s criminal souls, but created a symbiotic relationship so the human souls would also share in the testing process and have the chance to achieve communion with the Universe. But Cauchemar’s experiments upon himself had rendered him unsuitable as a host, and the aliens’ offer of freedom was no longer enough for him; he had fallen in love with a woman named Jasmine, and refused to leave without her...
The aliens expelled Cauchemar from this world when he refused to go, but he found his way back eventually, and was reunited with the woman who had been Jasmine. By that time, he’d passed through this region of space too many times, and was dying. He tried to save himself by taking genetic samples from “Jasmine”, but she was badly injured in the process, and when he tried to take her to the water mountains for help, the Creator’s defenses unmade her DNA. The Creator could not perceive Cauchemar, but his close proximity to Jasmine allowed him to share a moment of bliss as her entire life was made known to her. The devices he’s built using stolen genetic equipment are just putting off his own inevitable death, and being shot has hastened matters -- but he refuses to let the world he created go on without him, without being given the chance to know himself. Treena tried to kill him because she learned that he had kidnapped their child and grafted the fingers and hands of his other victims onto its body. He is now certain that Etienne hosts Jasmine’s soul, and he intends to take her and the baby to the Creator together. At the same time, Hox and the zombies will launch the final attack on the city, detonating dozens of bombs at once, killing hundreds before their time. The Creator will be flooded with hundreds of unscheduled souls, and when Cauchemar enters its presence with the baby -- a single entity with over two dozen godswitches grafted into its genes -- the Creator will break down completely. The backlash of energy will grant Cauchemar the revelation he seeks... and kill everyone else on this world.
The Doctor realises that Cauchemar is beyond reason, and threatens to set off the detonator core of the hospital bomb unless Cauchemar releases Braga. Cauchemar calls his bluff, and the Doctor flees -- but he pretends to attach the detonator wire to the doors, delaying Hox just long enough for the Doctor to locate Braga and flee outside. His friends have tracked down his signal and are waiting for him outside, but Cauchemar has planned for this and has planted a tracking device on Braga. Hox and his men locate the fleeing hover-car and attack it, and although Etty shoots Four-Four dead during the struggle, Hox and Cauchemar successfully kidnap her and escape. Now Cauchemar has everything he wants, and a head start to boot. The Doctor sets off in pursuit, and Vettul contacts the farm, telling the mooncalves to do what they can to delay Cauchemar until the Doctor arrives.
As Dark, Anji and Fitz study a city map, it occurs to Fitz that the numbers the zombies were given as identification must be the most important things they had to remember, and he realises that they’re map grid references. The points from the list Etty found map out the shape of a double-helix, Cauchemar’s last sick joke against the Creator who spurned him. The Holiest themselves have ordered that Dark is not to be punished for his recent transgressions, and he is thus able to convince Rammes to alert the authorities to the danger. In the meantime, since Four-Four was killed and Hox has had no time to replace him, Dark, Fitz and Anji visit the most prominent building in the Four-Four grid reference, in the hope that Hox himself has taken Four-Four’s place. Indeed he has, and Anji risks her life to distract and overpower him; when Fitz and Dark join in the struggle, Hox falls over the edge of a balcony to his death.
Upon arriving at the farm, Cauchemar forces Etty to carry the baby to the water mountains; but the mooncalves have blocked the path, and by the time they clear a way through, the Doctor has arrived. Cauchemar accidentally shoots and kills the baby while aiming for the Doctor, and Anji then calls him on Hox’s communicator. His plan has failed, and the final struggle was too much for his weakened body; he is dying, and will not reach the Creator’s Heaven. Enraged, he attacks the Doctor, but the seawater sluices up over his body, dissolving it away; the enzymes and catalysts in the holy water are the medium in which the Creator stores itself. With the last of his strength, Cauchemar pulls the Doctor over the edge of the cliffs with him to share his death, but the Doctor survives the fall and enters a healing coma. Anji and Fitz find him recovering at the base of the cliff a few days later, and they depart, off for new worlds.
On this world, or any other, faith is the medium for hope; whatever the afterlife holds, what really matters is what is done in this life. Dark has learned too much to remain a Diviner, and he thus remains on Etty’s farm, helping her to care for the mooncalves and till the land. Years later, he tracks down Lanna, in order to speak to her one last time; he’s dying, and he has received the Creator’s blessing. Thanks to his actions, the Creator has learned of the mooncalves and Cauchemar’s zombies, and has incorporated them into its Design. Dark’s faith has been restored as well. All life has meaning.