Industrial pollution has poisoned the Earth to the point of total environmental collapse, but there’s still time to do something about it. However, Mathew O’Hara of the Butler Institute has other plans, and the Doctor must stop him. To this end, the Doctor visits Ace’s friend Shreela in hospital, where she is dying of an auto-immune disorder brought on by the poisoned atmosphere. Since the Doctor last met her and saved her life, Shreela has become a respected science journalist, and the Doctor asks her to submit one final paper suggesting that certain blood proteins have been linked to the existence of telekinesis. This is not good science, and Shreela’s reputation is all she has left -- but she has only hours to live, and owes the Doctor what life she has had. She submits the paper, albeit reluctantly.

The Doctor then visits the King Building in New York, where he breaks into the offices of the Butler Institute. With the help of a disillusioned cleaning woman named Maria, he avoids two security men, Mulwray and Christian, who are going off duty after shooting a policeman named McIlveen and taking his body to the fifty-first floor. Maria helps the Doctor to hack into the Butler Institute’s mainframe, where he confirms his suspicions about what’s going on -- but he refuses to take Maria with him when he leaves, as she’s known what’s been happening here for some time and has done nothing about it. Shattered, she dies on the way home, finally giving up the fight against the poisonous cleaning fluids that have wrecked her body after years of work. The Doctor, meanwhile, goes after Bobby Prescott, a serial killer born from the anti-book riots, who lives in the ruins of the old city library and hunts the kids who spend their lives staring at videos and playing computer games. Some time ago, something frightened Prescott within an inch of his life, and the Doctor forces Prescott to tell him everything he knows about the terrible thing which is being kept in a grey drum in Turkey. Once he has everything he needs, the Doctor leaves Prescott to the mercy of the kid gangs he’s been preying on for years.

Stephanie, an ambitious employee of the Butler Institute, has been hacking into its mainframe herself in her spare time, to learn more about the company and improve her chances of promotion. Mulwray discovers her illegal activities and takes her to O’Hara at gunpoint to explain herself, but O’Hara praises her ambition and lets her in on the Institute’s latest top-secret project. For some time now, the rich and powerful have been harvesting organs from criminals and the homeless to ensure their own survival, but this is only a stopgap measure and it is now clear that the Earth will soon be unable to support human life. O’Hara has therefore put his team to work on a project to upload human minds into computers; when their work is complete, the entire human race will become software, running on computer systems in vast bunkers where they can survive the death of the Earth. Mulwray, who has never taken O’Hara’s claims seriously, is appalled to learn that O’Hara intends to submit his eight-year-old son Patrick to the process -- which effectively means killing the child. But Stephanie has no compunctions about joining O’Hara’s team, and Mulwray realises that he’s in too deep to get out now.

The Doctor, his research complete, sends Ace to Turkey and get the drum he needs. She needs to hire a group of Kurdish mercenaries to help her storm the island, and to buy their services, she sells them arms through the Doctor’s old friend Miss David. But when she tosses a grenade to their leader Massoud for him to inspect, he thinks it’s live and panics. Humiliated before his men, Massoud tries to kill Ace before their team boards the boat, but she survives the attack and drives him away, winning the others’ respect. While testing out a combat helmet before their arrival, she accidentally drops it, damaging the laser eye sight and ruining the helmet. The boat arrives on a quiet Mediterranean island, where Ace and her mercenaries easily overpower the defenders -- frightened American teenagers, unprepared for the reality of the situation, who had been playing VR games instead of watching for attackers. Despite the boys’ warning that the thing in the drum is evil, Ace takes it from them and arranges to have it sent to the airport and flown to England. She and the mercenaries then return to the mainland, but as she returns to her hotel, Massoud attacks her again and she is forced to kill him by burning through his brain with the damaged helmet laser.

Physically and emotionally exhausted, Ace sleeps through the night and then goes to the airport, where she is reunited with the Doctor and accompanies him back to the house on Allen Road in Kent. There, the Doctor opens the drum to reveal that it contains a chemically embalmed teenager, Vincent Wheaton, who was born with the ability to focus other people’s emotions into bursts of telekinetic power. When he and his friend Calvin were attacked by Bobby Prescott, Vincent drew upon Calvin’s fear and memories of Cthulhu Gate VR software, and transformed Calvin’s bicycle into a Lovecraftian monster which drove off the terrified Prescott. Unfortunately, this convinced Calvin that Vincent was a living gateway to hell, and he and his friends lured Vincent into a trap, anaesthetised him and sealed him in the chemical suspension drum.

Ace drags Vincent to the upstairs bathroom and washes the gel from his body, and as he slowly wakes, she and the Doctor go downstairs to await another arrival. Some time ago the Doctor had planted an article in an underground newspaper suggesting that his house was a gateway to other worlds, and this has drawn the attention of a young woman named Justine. When she was six, her friend was struck by a car and killed before her eyes, and the traumatised girl has since become fanatically opposed to pollution and the destruction of Earth’s environment. When she breaks into the house, finds Vincent and touches him, every car in the Doctor’s garage explodes. His weapon has successfully been tested. Justine believes that the Doctor is a sorcerer and that Vincent is channeling a demon, and although Ace scoffs at her beliefs, Justine points out that there’s no justification for Ace’s belief that the Doctor is a time-travelling alien. Ace is shocked to realise how easily Justine can demolish her own world-view, and she storms out of the house as Justine and the recovering Vincent make love.

The Doctor takes them all to New York for the next stage of the plan. Justine drugs Vincent and leaves his unconscious body in Central Park, where it is picked up by the Butler Institute’s Biostock Acquisition services. There, standard blood tests detect the presence of the proteins mentioned in Shreela’s article, and Vincent is therefore shipped directly to the project site for further testing. Meanwhile, the Doctor takes Ace and Justine to a drugstore in the process of being robbed by a street gang, but unfortunately Justine is so eager to be reunited with Vincent that she takes a drug and dies before the Doctor has a chance to brief her properly. The Doctor has arranged for McIlveen’s former partner Tessa Mancuso to respond to the drugstore robbery, but when she arrives she simply tries to arrest him without listening to his attempts to explain that there’s something odd about her new gun. He manages to get away from her, and when she pursues him Mancuso realises that he’s led her directly to the gang’s intended escape route. She and her new partner Breen arrest most of the gang, but Mancuso is attacked by a gang member who pops up from an unexpected direction -- and is shocked when her gun, a new model she’s been asked to field-test by the Butler Institute, shoots her attacker by itself before she even realises that there’s anyone there.

Ace is taken in for questioning, and spends an hour in a crowded prison cell only to be released when Stephanie intervenes on her behalf. Fortunately for Ace, Breen happens to see her being taken away, and when he learns that all charges against her have been dropped he intervenes and gets her away from Stephanie. The Butler Institute has made a deal with the corrupt cops who run the holding tanks; healthy prisoners who have not yet been convicted of crimes are quietly erased from the prison records and passed directly on to Biostock Acquisition for organ harvesting. Breen sends Ace back to Mancuso, who has finally agreed to listen to the Doctor -- who has something to tell her about her old partner. McIlveen’s death appeared to be a random gang sniping, but in fact his body was taken to the Butler Institute and used in the final wave of expermients for O’Hara’s project. His mind was uploaded into a computer chip -- and that chip is being used to run the artificial intelligence centre of Mancuso’s new gun. The Doctor connects the chip to a computer so it can communicate directly with Mancuso, who realises that the Doctor is telling the truth and agrees to help him stop O’Hara.

Any dead bodies found at the scene of a crime are automatically sent to the Butler Institute for harvesting, but since Justine took the drug too early, the Biostock Acquisition department has learned that she is still alive. Before they can kill her and harvest her organs, Mancuso helps the Doctor and Ace to storm the King Building and rescue her. They then head out to O’Hara’s project site, unaware that O’Hara has worked out what is happening and is lying in wait for them. O’Hara’s wife has learned the truth about the project, and O’Hara has killed her and sent Patrick to the project centre to be prepared -- but Mulwray has become distraught after witnessing the clinical murder of O’Hara’s son, and O’Hara and Stephanie decide to remove the firing pin from his gun as a safety precaution. When the Doctor and his allies arrive, Stephanie shoots Mancuso and uses Vincent as bait to lure the others into a trap. Before O’Hara can do anything to them, however, Mulwray snaps, pushes Justine towards Vincent and tries to shoot O’Hara. His gun does not fire, and O’Hara shoots him instead. O’Hara is too late to stop Justine and Vincent from touching, but all Vincent gets from Justine is her love for him, and he is unable to use that emotion destructively. The Doctor tells Vincent to run, but O’Hara pursues and catches him -- only to discover too late that it is not only Justine whose emotions can act as Vincent’s power source. As Ace watches in shock, Vincent hooks into the arctic cold of O’Hara’s emotional landscape and releases a blast of sub-zero air which kills Stephanie, reduces O’Hara to ash and destroys the entire project site.

This major setback puts an end to the project for good, and the global supercorporations thus have no choice but to put all of their funding towards an environmental cleanup programme while there is still time. The Doctor connects McIlveen’s chip to O’Hara’s automated medic and leaves it to tend to Mancuso. Vincent and Justine can no longer channel their power destructively -- but the weapon has served its purpose now, and is no longer needed.