The Doctor is feeling less than he was, following the removal of his second heart by Sabbath. As if to compensate for these feelings, he tries pushing the TARDIS to its limits, to see how far it’s willing to go for him. He pushes his ship too far, however, and must materialise in order to prevent it from breaking up. The external atmosphere is lethal, however, and he, Fitz and Anji require environmental filtration discs to filter out the dangerous toxins in the air; even the Doctor, who was once capable of shrugging off such extremes of temperature, seems to feel the cold as they emerge. Outside, they see the lights of a city shining across what seems to be a frozen wasteland, but as they approach the city someone runs past them and someone from the city shoots at the fleeing figure, causing the ice to break up around them. As something large pushes through the ice behind them, the Doctor and his friends realise that the city is not constructed on land, but on a framework of metal stilts; they’re on the frozen surface of a sea of acid, and it’s breaking up around them. They reach the city and climb up its struts in time to save themselves, but the TARDIS has fallen through the surface and is lost to them.
When the Doctor and his friends reach the city walkways, they find themselves surrounded by the local militia; their leader, Powlin, was shooting after a mysterious serial killer who has just decapitated another victim. Powlin questions the odd-looking strangers, decides that they are harmless, and leaves them to their own devices. The Doctor first questions him about the city, and learns that he and his friends are in the distant future, on the planet Hope, one of the largest population centres of the planet Endpoint. The seas are corrosive, the air is toxic, and the formerly human inhabitants of the planet have evolved to survive; amongst other traits, they have no body hair, their eyes are protected by an inner lid, and their lungs are much stronger than those of ordinary humans. Powlin regards the new arrivals as genetic throwbacks, but otherwise has little interest in them; the Endpointers concentrate all of their effort on the daily struggle to survive. At first, the Doctor wishes to help with the investigation into the murders, but when he, Fitz and Anji witness the casual violence around them, he realises that life is cheap here, and decides simply to concentrate on getting away as soon as possible.
A local merchant, Pazon, directs them to the Silver Palace, a casino where they will find the only man who can help them recover the TARDIS. The Doctor buys his way in past the bouncers with an apple core from his pockets; to him it’s the least impressive object in his pockets, but to the people of Endpoint it’s a sample of a species which hasn’t existed for millennia. Silver, intrigued, sends his second-in-command, Miraso, to question the newcomers; however, as she invites the Doctor to speak with Silver, a group of cybernetically enhanced fanatics, the Brotherhood of the Silver Fist, attacks the casino, threatening to kill all of its patrons unless Silver surrenders himself. Silver, who is himself cybernetically enhanced, defends his patrons against the Brethren, and the Doctor also joins in the fight -- only to discover, when one of the Brethren starts to throttle him to death, that he can no longer bypass his need to breathe as he once did. Silver drives the surviving Brethren out and offers to extend the credit of all those caught up in the attack; he then addresses the Doctor and his friends, and soon determines that they are indeed time-travellers. He thus offers them a deal; retrieving the Doctor’s “lost property” will put a great strain on Hope’s limited resources, and Silver will only do so if the Doctor helps him to investigate the mysterious decapitations which have been causing unrest and uncertainty amongst the city’s population. The Doctor reluctantly accepts the deal, although he suspects that Silver just wants the TARDIS for himself.
Silver gives the Doctor, Fitz and Anji temporary rooms in the Palace, and Miraso tells them about the history of Endpoint. This solar system was once the home of a thriving civilisation, but it was caught in the crossfire when two of the great factions of the Universe went to war. Whole planets were destroyed, and only Endpoint, which was literally the garbage dump of the system, survived. The few survivors were forced to make a new home here, build cities from the ruined remains of their civilisation, and adapt to survive in their harsh new environment. The Doctor finds hope in the fact that humans can survive even on such as world as this -- but what have they become? The bouncers at the Silver Palace were badly injured when the Brotherhood attacked, but Miraso has put them back to work right away. Does harshness breed harshness? The Doctor is haunted by nightmares in which he is the captain of a sailing ship in a void, and in which he orders his crew to open fire on the enemy -- unleashing terrible destruction with a single word and gesture...
There doesn’t seem to be a pattern to the killings, but the Doctor theorises that this means they are not ritualistic -- rather, they are part of some greater plan. When a family of four is killed and decapitated, the Doctor finds a disposable tranquiliser dart embedded in one of the bodies, evidence that the killer is not a native of Endpoint, where resources are limited and nothing is disposable. Meanwhile, Anji explores the Palace, and finds apple trees being fast-grown in the hydroponics laboratories from clones of the Doctor’s apple core; they have accidentally, innocently reintroduced an extinct species to the Universe. Anji also learns that Silver has a controlling interest in almost every business and “government” on the planet; if he expands any further, there will be nobody left for him to trade with. He’s accomplished everything he can on Endpoint, so what does he want out of life now? Fitz, meanwhile, wonders why the cybernetically enhanced Brotherhood of the Silver Fist claim to see the cybernetically enhanced Silver as an abomination. In order to investigate, he bribes Pazon for information, successfully contacts the Brotherhood, and claims that he wishes to join them.
Anji is unable to learn anything about Silver’s origins. In fact, his birth name is Humberto de Silvestre, and he was born in the 30th century, when the underpriveleged lived in the toxic waste dump known as the surface of the Earth. Humberto suffered from numerous birth defects, and in his teens he attempted to strike back at the uncaring upper classes by hacking into the worldwide military computer net. He was detected, but the military showed their appreciation for his skills by enlisting him, giving him surgery and cybernetic implants which saved his life. Just as he was beginning to make a name for himself, however, he was critically injured by another, more successful hacker-terrorist. His mother Maria gave her permission for the military doctors to use experimental alien technology to save his life, and they bonded his brain to a liquid computing medium which effectively turned Silver into a human computer. When the Earth was attacked in 3006, several of Earth’s best agents were sent through Time using experimental technology; Silver was sent into the distant future, to search for reinforcements or technology with which to save humanity. But even then, Maria knew that her son had become something other than human, and that he would not be coming back...
As the Doctor continues his investigation, only Fitz notices how tired his old friend appears; he no longer has the superhuman stamina he once possessed. He has, however, learned that the people of Endpoint are stronger than the human norm; in their brains is a vivactic gland which generates a rare hormonal cocktail named Kallisti. In effect, the people of Endpoint operate on a permanent adrenalin rush. Since Kallisti breaks down quickly on contact with air, it appears that the killer is taking the heads of his victims in order to ensure a constant supply of the chemical. In order to catch him, the Doctor decides to offer himself up as bait, a concept which would never have occurred to the people of Endpoint. That night, the Doctor and Fitz go out into the slums of the city, and are indeed attacked. The killer shoots Fitz with a tranquiliser dart, but the Doctor overpowers the figure and chases him out of Endpoint, across the refrozen surface of the sea to a waiting submarine. There, he overpowers the killer and discovers that he is an ordinary, if somewhat inbred, human. But the run across the ice has left the Doctor exhausted, and when the other humans in the submarine corner him and shoot him with tranquiliser darts, he finds that he is no longer capable of metabolising the drug out of his body.
Anji talks to Silver about his past and present, but he soon realises that she’s probing for more information. Eventually, she admits that she’s been thinking about her lover, Dave Young, who died without reason when caught in the middle of an alien war. If Silver can clone the extinct apple back to life, can he do the same for Dave? He admits that it is possible for him to create a human who is genetically identical to Dave, but the man would have none of Dave’s memories and would in effect just be a twin. Furthermore, the drain on Endpoint’s resources would be phenomenal, and he would therefore require something from Anji in return. Silver has accomplished all that he can on Endpoint, and wishes to leave; thus, he requests that when the Doctor’s TARDIS is recovered, Anji take a scanner on board and provide Silver with data with which he can construct his own time-travelling machine. In order to resurrect her dead lover, Anji will have to betray the Doctor.
Powlin reports that the Doctor has disappeared, but Silver reveals that when he and the Doctor shook hands on their deal, Silver injected a nano-tracer into the Doctor’s bloodstream. By draining the entire city for power for several minutes, causing havoc, Silver activates the planet’s satellite network and locate the Doctor somewhere on the sea bed. Silver undertakes the rescue mission himself, ostensibly in order to prove to the people of Hope that he is still in control, and that he is willing to risk everything on their behalf. His armour is fitted with protective shielding and propulsion units, and the people of hope watch as Silver dives into the toxic sea to rescue the Doctor.
The Doctor finds himself imprisoned in a deep-sea bunker by several humans who have recently awoken from cryogenic stasis. Their leader, Dr Stephens, regards the Endpointers as abhorrent mutations, suitable only for experimentation; he intends to isolate and reproduce Kallisti, strengthening his own species and returning the human race to its position of dominance in the Universe. The Doctor, disgusted, claims that the innovative, adaptable survivors of Endpoint have more claim to being human than these inbred bottom-dwellers, with their obsession with keeping “humanity” pure. His point is proven when Silver attacks the bunker; the humans, who had simply assumed themselves to be inherently superior, are utterly incapable of defending themselves against the assault. The Doctor isn’t pleased that Silver kills over forty of the bunker’s defenders, but the attack is successful; the bunker now belongs to Silver.
Meanwhile, Fitz recovers from his assault and renews his contact with the Brotherhood, but when he questions the inconsistencies in their “logical” faith, he creates a religious schism. Soon the furious Brethren are crying out for his blood, but then the image of their cybernetic Queen appears before them and orders them to release Fitz, claiming that he is an unworthy sacrifice. Fitz returns to the Palace, where he realises that the “Queen” is in fact Miraso in disguise. She admits that the Brotherhood is a sham organisation established by herself and Silver; it gives potential troublemakers an outlet for their dissatisfaction, and allows the public to see Silver ruthlessly putting down all resistance, while still remaining firmly under Silver and Miraso’s control.
While exploring the bunker, the Doctor and Silver find a set of forgotten terraforming pods, which can be used to transform the seas and atmosphere of Hope into something that humans -- and their descendents -- can breathe safely. Silver activates the pods, and the people of Hope are amazed when a storm breaks over their city -- and it rains actual water rather than acid. Soon, the skies are blue once again, the seas are safe, the TARDIS has recovered, and Stephens, the man behind the brutal killings, is in custody, ready to face trial. It seems that all has been resolved, but Miraso is disturbed by the rapid changes and fears that there will be no place for her in Silver’s new order. Fitz also fears that this has all been far too easy, and when he investigates a strange comment made by one of the Brethren, he discovers that Silver has imprisoned terribly mutated Endpointers in dungeons beneath the Silver Palace -- savage, feral people with a silver sheen to their skin. Meanwhile, Anji decides to act on behalf of Dave, who should never have died as he did, and thus trades the secrets of the TARDIS for the chance to give him a new lease on life.
The Doctor operates on Silver, removing a drop of the “liquid computer” from his brain tissue and merging it with the Kallisti, thus enabling Silver to reproduce the chemical. However, the Doctor is also disturbed by these changes, and when he questions Stephens, he learns that the bunker has a Hypertunnel, a means of escaping from this planet through hyperspace. When Fitz tells the Doctor about the mutants in the dungeon, the Doctor realises that Silver is even more ambitious than he’d suspected, and breaks into Silver’s office to investigate. There, he and Fitz discover that Silver has been studying a map of the galaxy, which shows all of the nearby planets from the Imperial throneworld to the dead planet A2756. Miraso catches them both, but she too fears Silver’s awakened ambitions and thus agrees to help them stop him.
Meanwhile, Anji realises that the Doctor is suspicious of Silver, and fears that “Dave II” will be caught in the middle if the Doctor and Silver become enemies. Silver agrees to take her to the bunker to see the final phase of Dave’s gestation, but although the clone is fully human, Silver refuses to awaken him. He’s kept the letter of his bargain with Anji, but intends to keep Dave in suspended animation as a source of genetic material with which to restore some diversity to the human race. He now has enough of the enhanced Kallisti to begin transforming the sleeping humans into “Silverati”, semi-synthetic soldiers imbued with the Kallisti/computer cocktail and programmed to be utterly loyal to Silver. His earlier experiments had failed, and the mutants in his dungeon are the result, but now, thanks to the bunker’s technology and the help of the Doctor, Silver has completed his work. Anji and her friends are to be transformed into Silverati as well, and Silver will then conquer the Imperial throneworld and use the data from the TARDIS to construct a fleet of time machines, spreading his power even further.
The Doctor, Fitz and Miraso travel to the bunker, where they discover what Silver is doing but are captured by Silverati before they can put a stop to it. Silver literally pins Miraso to the wall for her betrayal, has the Doctor searched, and locks up him, Fitz and Anji. Anji is forced to admit to the Doctor that she betrayed him, but she stands up for her principles; the Doctor has always championed the cause of the innocent, the weak and the helpless, and that’s all she was trying to do. The Doctor concedes her point and gives her his key to the TARDIS, refusing to let one betrayal spoil his capacity to trust his friends. He then reveals that he slipped a blasting charge into Fitz’s pocket when they arrived, assuming correctly that Silver would only regard the Doctor as a threat. There are two Silverati standing guard outside, but when the Doctor blows up the cell door the guards are badly injured and the shock breaks their programming. One Silverati, formerly known as Joshua Kent, tells the Doctor that Silver is trying to reactivate the Hypertunnel. The Doctor leaves them where they lie, knowing that the enhanced Kallisti in their bodies will soon heal their injuries, and once healed they leave the bunker of their own accord and are not seen again.
The Doctor frees Miraso, and sends her with Fitz to secure a submarine for their escape. He has a plan to deal with Silver, but it involves reprogramming a sample of the enhanced Kallisti and temporarily transforming Dave into a Silverati with no loyalty to Silver. He refuses to do so without Anji’s permission, however, which she grants. When Dave awakens, he knows what he must do, and he thus accompanies the Doctor to the Hypertunnel. The Doctor tries to distract Silver while Dave fights his way past the other Silverati and apparently tries to shut down the Hypertunnel. Dave is overpowered, and Silver nearly kills the Doctor, but Anji shoots Silver through the eye with a tranquiliser dart gun. In agony, Silver flees through the Hypertunnel, taking his army of Silverati to the Imperial throneworld, along with the stolen data which will enable him to construct a TARDIS. Or so he thinks. In fact, the Doctor removed the memory wafer from Silver’s data pack while they fought, and Dave has redirected the Hypertunnel using co-ordinates which the Doctor picked up from the map in Silver’s office. Silver and his army are now stuck on the dead world A2756, with no way off.
Endpoint has been changed forever by these events. The environment is now safe and non-toxic, humans and Endpointers have been reunited, and it’s up to Miraso to guide her people towards a brighter future. Dave is human again, as the Doctor had programmed the Kallisti to break down after a day had passed. He’s not the Dave Young whom Anji knew, but there’s enough of the old Dave about him for Anji to bid him a proper goodbye, and she is thus able to set her past to rest before she leaves with the Doctor again.