After taking Ace to her friend Julian’s funeral, the Doctor travels several centuries into the future to check out a book from the Joycetown library on the planet Heaven. The librarian, Fyan Trench, seems oddly ill at ease, and claims that the book which the Doctor wants is missing. On the streets of Joycetown, Ace meets a Traveller named Jan Rydd, whom the Doctor saves from a bullying soldier named Kale. Ace and Jan are immediately attracted to each other, but the Doctor advises Ace not to get involved with Jan, telling her she’ll only get hurt. Ace, upset that he seems to think she can’t take care of herself, goes to the Travellers’ camp while the Doctor tries to speak with Miller, the head of the military forces on Heaven. At the camp, Ace meets Jan’s friend Bernice “Benny” Summerfield, an archaeologist excavating a native structure. Apart from a few sites such as this, there is no other evidence of Heaven’s former civilisation, which vanished centuries ago without leaving a fossil record; the Earth and Draconian Empires have thus set aside Heaven for use as a graveyard and memorial for those killed in the Dalek wars.

Ace learns that Jan has an open relationship with another Traveller, Roisa, but she decides that he’s too smug for her and walks Benny back to the dig. On the way, Ace tells Benny about her travels with the Doctor, and they meet the Travellers’ sexless high priest Christopher as he meditates in preparation for their conference on the Great Wheel. He is disturbed, however, by the sense of some great evil lurking just outside his perception. Meanwhile, Roisa goes for a walk outside the camp, upset with Jan for flirting with Ace -- but while alone she is contacted by Brother Phaedrus of the Vacuum Church, which believes that life is ultimately meaningless. Roisa stepped on an odd filament of fungus some time ago, and Phaedrus has bad news for her.

Miller has heard of the Doctor from the Draconians, who call him “the Oncoming Storm”. He thus tells the Doctor all he knows about a vast mottled sphere which has recently been spotted in local space, and which has always vanished before contact can be made. Fearing he’s left things too late, the Doctor visits Benny’s dig, produces a tesseract which vanishes before her eyes, and uses a Gallifreyan perigosto stick to unlock the structure she has been excavating. Inside, they find a buried observatory and the remains of a bear-like alien who apparently manacled herself to the wall after eating a note she had written. The Doctor is unable to decipher the writing, but the dust about the body smells of mushrooms, confirming his worst fears. As he and Benny return to Joycetown, somebody tries to kill them, and although Benny manages to shoot off the attacker’s arm, the attacker still flees before he, she, or it can be identified.

Ace returns to the Travellers’ camp, and agrees to accompany them into virtual reality for their conference on the Great Wheel. Most of the Travellers, including Jan, have installed direct neural jacks into their bodies, but Ace must wear a headset to enter Puterspace. There, in the Land Under the Hills, Ace and Jan meet the Trickster, a god who shows Jan a goblet which always refills itself with blood. Jan stole the real goblet from the Vacuum Church to protest their acceptance of sacrifice, a concept he can’t cope with because of what Christopher did for him. They were both drafted to fight the Daleks, but chose instead to volunteer for drug tests -- and when Jan lost his nerve at the last moment, Christopher took most of Jan’s drugs as well as his own. He acquired astounding psychic powers but lost his gender in the process, and Jan, who only took a few drugs and became mildly pyrokinetic, has never forgiven himself. He and Ace continue to the Great Wheel, where the despairing Roisa unexpectedly asks her fellow Travellers to leave Heaven and let her remain here, alone. Before they can ask why, the Wheel is attacked by a mottled sphere, which can only have penetrated their domain if someone on the inside let it in. Christopher uses his powers to hold it off while the others escape, but is killed before he can disengage.

The Travellers bury Christopher’s body and light a pyre for him, and Ace spends the night with the grieving Jan while Roisa seeks comfort with her other lover, high priestess Maire. Later, as Ace sleeps, she dreams of the Doctor offering himself as a sacrifice to Death; he knows how many she intends to take on Heaven and begs her to take him instead of Ace. Death rejects the deal -- but has he another to offer in his place? Ace awakens the next morning and returns to town, where the Doctor seems oddly unsettled to learn that she slept with Jan, and asks her to find out what she can about the book he came to collect. Trench still seems nervous talking to her, and she realises that he is being monitored -- but despite the risk, he tells her that the book she wants may be listed on the library computers, although he’s far too busy to look it up for her now. She understands, and is grateful. Meanwhile, Kale reports to Miller with his arm in a sling, claiming to have been attacked by a group of Sontarans, and Miller agrees to let him take a shuttle to the orbital platform to scan the planet for any other alien patrols.

The Doctor speaks with Jan, and realises that he cares deeply for Ace. Hoping to find another way to defeat the enemy, the Doctor jacks into Puterspace himself, where he discovers that in recent years every dead body in human and Draconian space has been sent to Heaven; there is an army of the dead buried beneath the world, awaiting collection. He is attacked by assassins from the Vacuum Church, but is saved by Christopher, who was able to cheat death temporarily by using his powers to upload his mind into Puterspace. He knows what the Doctor has planned -- and also knows that it is too late to defeat the enemy by any other means. Before the Doctor can leave Puterspace, Phaedrus catches him in a software trap which forces him to relive his third incarnation’s long, slow, agonising death from radiation poisoning, but Ace arrives in the Travellers’ camp, sees his predicament, and enters Puterspace herself to rescue him. When she does so, the software trap transfers them both into Ace’s worst memory instead of the Doctor’s, and they find themselves in Perivale. There, they meet Ace’s dead friend Julian, and realise that his mind was absorbed into the enemy’s group consciousness after his death. The Doctor is able to restore Julian’s individuality, and Julian is able to restore Christopher from beneath the Perivale simulation. Phaedrus enters the trap himself, sends Julian back into the group mind and tries to kill the Doctor, but Ace snaps his link to the real world and he is forced to relive his own worst memory -- when he euthanised his own dying mother. Christopher guides the Doctor and Ace out of Puterspace, and as the Doctor recovers from his ordeal, Roisa gives him a drink from the goblet which Jan stole from the Vacuum Church.

That night, the Doctor and the Travellers break into the library, where they find acolytes of the Vacuum Church threatening Trench. The Travellers try to drive them off, but the acolytes are no longer entirely human and can survive even direct shots from the Travellers’ blasters. Trench, knowing that he is finished, tells the Doctor that Benny has the book he’s looking for -- and then transforms into a mobile fungus which attacks them all. The Doctor sets the fungus creature on fire and flees with the Travellers, just as Miller arrives with news of the Sontaran invasion. He learns too late that Kale lied -- his “arm” was in a sling because Benny shot his real arm off earlier. Under the influence of the enemy, Kale has infected the crew of the orbital platform with fungal spores and put it out of commission. Reinforcements won’t arrive for a week, and until then, Heaven is defenceless.

On their way to the dig, the Doctor once again tries to dissuade Ace from her romance with Jan, and she realises that he’s jealous and afraid of being left alone. He collects the book from Benny and finds a note from himself inside, written by a future incarnation, giving him the key he needs to translate the writing in the Heavenite observatory. As he sets to work, Benny and Ace talk, and Benny tells Ace that her father was accused of cowardice when he vanished during a battle with the Daleks, while her mother was killed when the Daleks attacled her home colony. Benny was drafted into Spacefleet, but, unable to deal with the regimented life, she went AWOL and faked her archaeological credentials in order to shelter with a dig. She isn’t really a professor, but she has worked as an archaeologist for years, exploring human space and hoping one day to find out what really happened to her father. Ace returns to the Travellers’ camp to spend the night with Jan, who tells her his secret name; Aradrath, “the one big fire”, which he hopes to light one day with his powers. Later that night, shadowy figures on the edge of the campsite release spores into the camp, and some of the Travellers are infected before Ace can sound the alarm. Even later, Christopher enters the camp, having used his neural link to Puterspace to reanimate his dead body, and delivers a warning to Ace; if she chooses to remain with Jan, she will have to make a sacrifice…

The Doctor translates the writing in the observatory, which confirms all of his worst fears, and has Benny take him to the graveyards -- where they find that every body buried on Heaven has been infested with the fungus. Although it means risking damage to artefacts buried around the observatory, the Doctor asks Benny to dig it out completely, as quickly as possible -- before he has to do something he’ll regret. Kale tries to crash the orbital platform into the dig to stop them, but the Doctor takes Ace and Benny to the Vacuum Church to confront Phaedrus, and Ace, fearing for Jan’s life, threatens to kill Phaedrus unless he calls off the attack. The enemy still needs Phaedrus alive, and they self-destruct the platform before it crashes. The Doctor finally identifies the enemy to the Travellers as the Hoothi, a race of intelligent fungi which were believed to have fled the galaxy millions of years ago after an abortive attack on Gallifrey. The Hoothi feed on death and decay, and travel in giant organic spheres filled with toxic gases. They are master planners, laying traps for their foes centuries in advance; everyone infected with a spore is now linked to the Hoothi group mind, and the Hoothi can see whatever they see, control their bodies, and transform them into fungus warriors with a thought. There is no cure.

Benny’s team digs out the observatory, and the Doctor uses the superstring telescope inside to locate the Hoothi sphere -- but Heaven is now defenceless, and the Doctor seems to give up all hope of stopping the Hoothi before they arrive for their harvest. Roisa straps explosives about her body and rides into Joycetown to destroy the Vacuum Church, but finds that she is unable to pull the detonator; her arrival has been expected, and Phaedrus takes her to the crypt to meet her new masters. Jan, realising that Roisa has been infected and furious with the Doctor for doing nothing, decides to take action himself. He enlists the aid of his friends, and although he tries to leave Ace behind to protect her, Ace and Maire work out where he’s going and follow him, determined to help. Together, they steal a Draconian ship and launch it into orbit, intending to disguise it as a derelict, use the superstring telescope to locate the Hoothi ship, and ram it. As they approach the sphere, Ace asks Jan to marry her, he accepts, and Maire witnesses their betrothal. And then the Hoothi sphere comes into range, and everyone except Ace and Maire explodes into fungus -- including Jan. Ace and Maire escape in separate pods, and as Ace falls towards Heaven, catatonic with grief, the Doctor’s tesseract drops into her hands, a fold of time and space which seems to have captured the essence of Jan and which pulls Ace back from the edge of madness. Maire’s pod crashes into the Vacuum Church, but fails to bring it down or kill Phaedrus.

Benny tries to talk sense into the Doctor, but he seems too weighed down by the evil he faces to be of use. He explains that the Heavenites worshipped the Hoothi as gods, and reshaped their planet into a trap -- and the Hoothi harvested the entire race once their work was complete, all but one brave astronomer who defied her gods and left a warning for those who would follow her. He then learns that Ace has followed Jan, and is horrified, as he’d been certain that Jan would find some way to stop her. He immediately sets off to confront the Hoothi, and Benny joins him as he pilots the TARDIS to the sphere, a noxious organic Hell in which decaying corpses serve the giant master fungi. The Doctor gives the Hoothi one chance to surrender, but they mock him; they have planned for centuries to raise an army of the dead with which to conquer Gallifrey through force of numbers, and Roisa slipped a spore into the stolen goblet before offering the Doctor a drink. They can make him one of theirs at any time they wish. They will, however, allow him and Ace to leave unharmed if he agrees to destroy Heaven’s communications equipment. As the Doctor and Benny leave, they see Jan’s dead body walking in to join the rest of the Hoothi’s slaves.

The Hoothi’s preparations are now complete, and the harvest begins. All those infected with the spores are transformed into fungus, while millions of bodies rise from their graves and march on the cities. The Doctor sends Benny back to the dig to look for Ace, who has landed safely in the forest and is heading for the Vacuum Church, seeking revenge. Christopher finds them as well, and assures Ace that Jan was not manipulated into his death but went of his own free will; however, Benny is an expert at reading body language, and knows that he is lying. Meanwhile, Phaedrus, satisfied with his work, connects himself to Puterspace to make peace with his mother; he has borne the guilt of her death for years, and has now brought death to Heaven on a grand scale, showing all the true meaninglessness of life. Ace finds Phaedrus in the Vacuum Church, and plugs herself into Puterspace to follow him and avenge Jan’s death.

The Doctor convinces Miller to deactivate Heaven’s communications, and as soon as he does so, the Hoothi sphere arrives above Joycetown to collect its army. As the dead march into the Hoothi sphere, the Doctor goes to the Vacuum Church and jacks into Puterspace, ostensibly to pull Ace out so they can escape. But as Ace watches in horror, the Doctor and Christopher use Phaedrus’ link to the Hoothi, their own links to Puterspace, and Christopher’s old friendship, to contact Jan’s remains through the neural link still embedded in his fungus-ridden body. There is still a bit of Jan left in the Hoothi group mind, and the Doctor reminds him of his secret name -- and Jan starts the one big fire he had always dreamt of, using his pyrokinesis to ignite the gases within the Hoothi sphere. The sphere explodes, releasing the dead from the Hoothi’s grasp and saving the lives of all those remaining on Heaven. But Ace emerges from Puterspace knowing that the Doctor only pretended to give up, to manipulate Jan into entering the sphere so he could destroy it. He has saved the galaxy -- by sending the man Ace loved to his death.

Later, as the people of Joycetown deal with the aftermath of the invasion, Ace wanders back to the Vacuum Church in a state of shock and finds Phaedrus in the cellar, sacrificing himself to the last of the Hoothi. It has been waiting in the crypt as a backup in case of failure, and it now forces Roisa to herd Ace towards it at gunpoint; soon it will regain its strength and set new plans in motion. Maire, however, crawls out of the wreckage of her pod and shoots Roisa, and Ace calls on the remains of Julian within the group mind. Once, on Earth, she and Julian drove off the edge of their map into uncharted territory, only to find a prison there -- but beyond the prison was a beach, and freedom. Julian resists the control of the last Hoothi, and its body explodes into a fungal paste. Heaven is freed at last.

The Doctor has left Heaven to wander the Vortex, but when he returns for Ace, Christopher finds him and dies in his arms to show him just what he has done. The Doctor tracks down Ace and tries to apologise to her, claiming that his biology is strange at the moment; he could only fight the Hoothi now, while his mind was confused and they were unable to read his intentions. But Ace knows that he was in fact jealous that Jan would take her away from him, and she storms out of the Doctor’s life, taking only the tesseract to remind her of Jan. Benny isn’t pleased with the Doctor either, but she does accept that he did what he felt he had to and that he feels utterly wretched about it. The Doctor needs someone to travel with him, to remind him of who he is, and to give him a reason to fight the evil in the Universe; and since there’s nothing left for her on Heaven, Benny agrees to travel with the Doctor instead. For a time.