Several centuries ago, a human colony ship was expelled from warp space into the Elysium system, stranding the colonists light years away from the rest of humanity. Ever since then, power in the system has been held by the Founding Families -- but now a group of Reunionists who wish to forge links back to the rest of humanity is challenging the Families’ rule, and the result could be civil war. The key to the struggle could be the alien Artifact, a giant hollow world with a self-contained ecosystem, and with gravitational anomalies which could provide a short-cut back to human space. Benjamin Green, an agent of the Founding Families, is sent to the Artifact to find the elusive scientist Mark Bannen, to find out what he knows about the Artifact and force him back to the Elysium system if necessary. Green is welcomed to the Artifact by the science team sent to study its interior, and learns that they have recently made a breakthrough in their study of the Artifact -- but to preserve the Artifact’s secrets, Bannen blows up the expedition’s base, killing them all. Bannen then walks off into the depths of the Artifact as plant life seeps into the dying Green’s wounds, changing him beyond recognition…

The TARDIS materialises inside the Artifact, and Benny and Ace set off to explore the hollow, weightless interior while the Doctor lags behind, concerned by an odd sensation -- as if he is being hunted by something. Benny and Ace are attacked by predators which try to eat Benny alive; fortunately, her flesh proves poisonous to them, but she is badly injured and her wounds become infected. Ace tries to return to the TARDIS, only to find that it and the Doctor have both vanished. While passing through a clump of vegetation on her way back to Benny, Ace encounters a group of tiny metallic insects, and pays them little attention -- until they burrow beneath her skin… Meanwhile, the Doctor finds Benny lying near the remains of the previous expedition, and gives her a drug which cures her infection. They then investigate the destruction around them, and find Green’s briefcase and his notes warning of the imminent civil war.

An expedition of university students arrives on a routine tour of the Artifact, but Rhiannon, the only one of them to have visited the Artifact before, becomes entranced by its interior. Her friend Gail starts to become worried by Rhiannon’s behaviour, but before she can find out what’s wrong the entrance to the Artifact irises shut without warning, crushing one shuttle and trapping the other inside. While Captain Urquhart and his second-in-command Drew try to repair the damage to their shuttle, Gail tries to speak with Rhiannon, who reveals that she felt inexplicably satisfied when the second shuttle was destroyed. Gail discovers that the fungus growing on the walls of the Artifact is changing species when Rhiannon touches it; the fungus’ DNA is altering, which should be impossible. The fungus then expels a cloud of spores which envelops Rhiannon and Gail, and while trying to rescue them, the hapless Drew loses control of his skimmer and crashes near the Doctor and Benny.

Ace finds her way to the students’ shuttle, just as a predator emerges from beneath the Artifact’s central ocean and begins to slaughter the terrified students. The Doctor, Benny, Gail and Drew arrive, and the Doctor tries to communicate with the predator, noting that unlike most carnivores it is killing indiscriminately without pausing to eat. The predator starts to attack him, but then draws back, and before the Doctor can determine why, Ace and Gail kill it. Rhiannon falls into a coma, and the pollen from the altering fungus then seems to attack the Doctor -- who feels his own mind being assaulted by some unknown force. He therefore shuts down his mind, but as Benny tries to get his unconscious body to safety in the shuttle, a storm strikes and she is knocked out by a floating rock. Both she and the Doctor drift off, unconscious, into the depths of the Artifact. Rhiannon then awakens and deliberately leaves the shuttle, hoping that her former friends will understand the Artifact’s true beauty before they have to die. Drew tries to follow her, Gail tries to follow him, and Ace follows them both. Ace finds Drew, who admits that he suffers from epileptic seizures and lied on his application form so he would be permitted to become a space pilot; together, they set off in search of Rhiannon. Gail, meanwhile, finds and wakes the Doctor, who realises that whatever was hunting him has withdrawn its attention -- and theorises that it turned back to Rhiannon when he made himself unavailable.

Benny recovers in one of the Artifact’s rim forests, where she is attacked by a herd of primates with the ability to generate microwaves and cook their prey on the move. She is saved by the former Benjamin Green, now a mutant with no memory whom she dubs Midnight, and learns that the primates are in fact intelligent and are called “Builders”. She therefore concludes that they are the degenerate remains of the species which constructed the Artifact. The Builders take her to their city, a floating village constructed out of the Artifact’s plant life, where she observes the funeral of a Builder whom she killed in self-defence when she was attacked. The Builders microwave the dead Builder, and Benny eats of its flesh to be polite. She then witnesses the bizarre suicide of several Builders, who are overcome by a compulsion to fling themselves into a “deathpool” -- a bubble of water centred around a gravitational anomaly in the heart of the city. Elenchus, one of the more intelligent Builders, tells Benny that this compulsion has come over many of them in recent years, and asks her to help investigate by taking him to the planet where life originates. She is surprised to learn that he means a planet within the Artifact itself…

The Doctor and Gail construct a makeshift raft with which to navigate the Artifact’s ocean, and as they do so, Gail tells the Doctor more about the politics of the system and the looming threat of war. The Artifact itself has never been fully explored, as it is too large, and the conservative Founding Families, desperate to hold onto their imagined utopia, have discouraged any pioneers. It is suspected that the Artifact may extend into warp space, which might explain why the colony ship crashed in the first place. The Doctor and Gail are separated when their raft is caught up in a storm and collides with the Builders’ city, and Gail is nearly enveloped by an advancing wall of protoplasm which absorbs everything it touches. She escapes when a burning hut sets the advancing protoplasm on fire, burning a hole through the wall -- but although she drifts through safely, some of the protoplasm splatters onto her arm. Benny and Elenchus find her and burn the infected flesh away, but when Benny scans Gail’s arm with her medical kit to ensure that it is now free of infection, they discover that the protoplasm was transforming her DNA into a familiar pattern; when Rhiannon’s touch transformed the fungus of the rim forests, it changed in exactly the same way…

Despite the incredible size of the Artifact, Ace somehow locates Rhiannon floating amongst the giant mushroom trees and fungus of the rim forest -- and as the parasites under her skin begin to writhe, Ace realises that she has formed some sort of mental connection with the Artifact, just as Rhiannon has done. Mark Bannen then arrives and questions them, and is shocked when Ace recognises him and tells him that she met his father on the moons of Lucifer. He decides to show them how to use the Artifact’s gravitational discontinuities to travel, and Ace is thus able to take Drew and Rhiannon back to the shuttle. The rock storm has caused the already damaged shuttle to crash into the central ocean, and as it is swept along by the current, Rhiannon enters the living quarters and shoots tendrils out of her body, killing all of the remaining survivors. The shuttle passes through a massive gravitational discontinuity at the end of the ocean and emerges on the surface of a world made entirely of water, at the end of a string of stars.

Benny, Gail and Elenchus survive another storm, but Elenchus then leaps out of their raft and tries to drown himself. Benny collapses while rescuing him, but Bannen arrives and pilots them safely through another gravitational discontinuity into the second chamber of the Artifact -- where there is indeed a planet. There, he and Gail determine that Benny has a hairline fracture of her skull and internal bleeding, caused when she was struck by the rock in the earlier storm; the pressure has been building all this time and will soon kill her, and Bannen thus drills a hole through Benny’s skull to relieve the blood pressure on her brain. Gail also discovers that her arm is still infected by the protoplasmic DNA, and Bannen thus amputates it. It takes Benny several days to recover, but when she does she confronts Bannen, demanding that he explain what has been happening. He therefore informs them that the Artifact is not a construct at all, but a gigantic living organism. This planet is its egg, and the changes they have encountered are all a part of its natural life cycle. Rhiannon has become a vital part of this cycle -- and if she dies then the Artifact will die with her.

Rhiannon loses consciousness when the shuttle emerges on the surface of the water world, and Ace is temporarily freed from the Artifact’s control. Her connection to the Artifact has given her an understanding of its life cycle, and she explains to Drew that it used the gravitational discontinuities to transport water from other worlds through itself to other points in space, thus creating worlds like this one which eventually collapse under their own weight and become stars. Ace shuts off the oxygen supply to Rhiannon’s brain in order to give herself time to explain this to Drew, but leaves it too late and is unable to revive Rhiannon. She and Drew are thus forced to return alone to the shuttle, and pilot it back down into the depths of the water world, hunting the end of the discontinuity which brought them here. They manage to get back into the Artifact just as the nuclear reactions begin and the water world is transformed into a star, but they are a fraction of a second too late, and return to the Artifact dying of radiation poisoning from the burst of gamma radiation that sleeted through them at the moment of starbirth.

The Builders’ city is drawn into the planetary chamber by another storm, and Benny, Gail and Bannen are thus reunited with Midnight -- who informs them that the Doctor has been possessed by the Artifact, just as Rhiannon was before him. Midnight finds that he can use his new body to manufacture neurochemicals which transform the rim fungus into new species, and Gail thus collects some fungus which he can use to create a cure for Ace and Drew. When she returns to the city, however, she is surprised to find that her sample bag is now filled with the tiny metallic parasites, schill, which are apparently feeding upon the fungus. The atmosphere in the Artifact is changing, becoming similar in composition to the gas giants of the Elysium system, and Ace realises that the Artifact has entered a new stage of its life-cycle. It has finished manufacturing stars and is now putting gas giants in orbit around them, to act as incubators for its planet-sized eggs. This stage of its cycle requires intelligence, which it normally acquires from the species that have evolved within itself during its water-world stage, having used predators to cull any creatures intelligent enough to threaten its own survival. But this time, it infected Rhiannon instead of one of the Builders, and now that Rhiannon is dead it has infected the Doctor. Thanks to Ace, the Artifact has acquired the Doctor’s intelligence, and it may find a way to speed up the world-generating process -- and thus plant enough eggs within its lifetime to overrun the Universe.

Benny has been infected by a parasite due to her eating the Builder’s flesh at the funeral, but Ace injects her with poison, causing her body to form a cyst around the parasite; she then cuts the cyst free and has Midnight synthesise an antidote. As she recovers from her own radiation poisoning, she realises that the rim fungus is the equivalent of the Artifact’s neural system, which is why it began to change when Rhiannon touched it. If Midnight can synthesise the appropriate chemical agent, they can literally change the Artifact’s mind, tricking it into believing that it’s at a different point in its life cycle; then, it will release its hold on the Doctor’s mind, and he can take them to safety in the TARDIS. Bannen, however, holds them all at gunpoint, refusing to permit this. He has gained near-immortality through his symbiotic link with the Artifact, and identifies more with it than with the humanity that tore his mother apart during the famine riots in Mexico. He killed the previous expedition in order to stop the Elysium colonists’ war from disrupting the Artifact’s life cycle, and he’s willing to kill the others for the same reason. Midnight has already begun the change, but as Bannen shoots and kills Midnight, the Doctor awakens and drives Bannen off before he can kill anyone else. Unfortunately, Midnight has erred -- and thanks to his alterations, the Artifact is now dying.

As the rim forests begin to break up, a spark ignites the methane atmosphere, and an eruption of flame engulfs and kills the Artifact’s egg. The Doctor decides to use the TARDIS to manipulate the Artifact into forming a cyst around its dead egg and expelling it from its body; once outside it will become a planet, on which the surviving Builders can establish themselves as a species. Bannen, however, is waiting for the Doctor back at the TARDIS, and he informs the Doctor that the Artifact had already planted a clutch of eggs in the Elysium system; they will soon hatch, and begin to draw water away from the inhabited planets, resulting in the deaths of the human colonists. The Doctor is unwilling to permit death on such a scale, but Bannen tells him that the Artifact’s eggs were here first; from its perspective, the colonists are the parasites on its home. He shoots the Doctor through the chest, and then waits for the Artifact to die.

The others survive the dead egg’s expulsion from the Artifact, but Drew and Gail are then killed by a predator on the surface of the new planet. Ace manages to carry Benny’s unconscious body to a nearby beach, where the Doctor is recovering from his wounds inside the TARDIS. As she arrives, Ace realises that she and Benny are both still carrying parasites, and realises that the parasites are another stage of the schill -- which are themselves another stage of the rim fungus. When the Builders eat the schill they become infected, and the chemical changes force them to jump into the deathpools, which transport them to the egg, which the parasites fertilise. Ace and Benny were infected because Midnight used the rim fungus to cure them. The Doctor can save Ace and Benny from the parasites within them, but as Bannen pointed out, he can’t save the people of the Elysium system without destroying an entire alien species which has just as much right to exist. He and his companions are thus forced to depart, leaving the colonists to their fate.