The TARDIS enters a strange region of space-time where the normal laws of physics do not apply, and the Doctor casually informs Anji that it could take them days or even years to pass through this zone. To calm down, Anji visits the Stellarium, an observation chamber which takes the form of a glass dome looking out into the Vortex. There, she and Fitz see a swarm of Vortex Wraiths, a life form wholly alien to anything in the ordinary Universe. The TARDIS supposedly has safeguards which prevent the Wraiths from seeing it; however, they do, and impossibly seem to smash straight through the Stellarium dome and invade the TARDIS. Anji and Fitz flee to the console room, pursued by an army of Wraiths -- or rather by the hideous physical forms which the Wraiths have generated for themselves by corrupting the TARDIS’ control systems. As the creatures are about to burst into the console room, the Doctor has no choice but to materialise on the nearest inhabitable planet so he and his companions can flee...

The planet in question is Shakrath, which believes itself to be the centre of an Empire which extends throughout this sector of space. Since it is impossible to travel faster than light in this region, communication between the worlds of the Empire is conducted via the Pylons, or Engines of Transference, matter transmitters which exist on every civilised world. Civilised is a relative term, however; for example, on Shakrath the tattoos which identify a man’s Soul when he is reborn in a new body at the end of his journey are branded onto his face without the aid of anaesthetic. The nature of the Empire means that most worlds must take the long view of things; for example, the Ambassador sent from Shakrath to the planet Tibrus to negotiate a new trade treaty departs knowing that the results of his negotiations will not be known on Shakrath for over two centuries...

When the TARDIS materialises in the Plaza of the Nine Wise Maidens, and the monstrous Vortex Wraiths burst out into the crowded marketplace, the response of the Emperor’s private army (who are officially the palace musicians) is devastating and indiscriminate. The Doctor manages to get Fitz and Anji to safety as the Bandsmen open fire on the Wraiths and any ordinary citizens who happen to be in the way. Although they escape the worst of the fighting, they are placed under arrest, and the Doctor is brought before Morel, Ambassador to the Court of Shakrath. According to Morel, the Empire has relied on Transference for millions of years; but for some time now, monstrous creatures have been emerging from the Pylons. Although the Bandsmen have always destroyed them swiftly, the common people cannot be permitted to know of their existence for fear that they will lose their trust in Transference and the Empire will thus fall apart. Merely by arriving in the manner in which he has, the Doctor poses the greatest threat the Empire has ever faced. Morel therefore insists that the Doctor explain the function of his TARDIS, or watch as his companions are tortured to death.

Fitz and Anji have been thrown into a cell with Jamon de la Rocas, a professional rogue and miscreant whose attitude is so hearty and oratorical that for a moment Fitz thinks the Doctor has regenerated. Anji and Jamon don’t get along at all, and later Jamon will realise that this is due to his unconscious assumptions; as neither Anji nor Fitz show the brands of Transference he assumes them to be natives of Shakrath, servants or slaves to this “Doctor” of whom they speak. Also, the Empire’s track record in female emancipation is not worth speaking of; as a result Jamon’s attitude towards Anji is condescending at best, and he’s quite taken aback by her response. When the guards arrive to take the Doctor’s companions to an audience with the Emperor, Jamon is swept along as well, and he and the Doctor hit it off almost immediately; but Jamon is rather less pleased to learn that he’s on the planet Shakrath. When he last Transferred, he did so steps ahead of an angry local militia and was forced to jump blindly. He has heard rumours of the planet Shakrath, and realises that he and his new acquaintances are in for a hard time...

Officially, all visitors to Shakrath are treated with respect and honour, and thus the Doctor and his friends are warmly welcomed by the Emperor -- but only so this welcome can be recorded for posterity. Once the ceremony is over, Morel switches off the hydraulic Emperor statue he was operating and reveals that the assembled “dignitaries” who witnessed the ceremony are in fact slaves with their mouths sewn shut and their nervous systems wired to generators. The new arrivals are marched through a series of torture chambers to an audience with the real Emperor, a hedonistic man corrupted by a lifetime of debauchery. His bodyguards have been mutilated to make them stronger than any ordinary man, his harem girls’ mouths have been sewn shut, and the furniture in his private boudoir is made of human skin and bones. He decides to add Anji to his harem, and when Fitz protests, the Emperor orders that he be made a eunuch so he can watch over her. The Doctor decides that something must be done -- and Jamon gets the impression that he’s talking about the Empire as a whole...

At the Doctor’s request, Jamon provides a distraction while the Doctor nips about the Emperor’s boudoir, carefully repositioning various items within. In this area of stunted space-time it’s possible for the Doctor to manipulate the effects of probability to an extent, and the items the Doctor has moved interact in a Rube Goldbergesque series of accidents which allows the Doctor and his friends to escape while the guards trip over things and shoot each other. As the Doctor tries to lead his friends back to the TARDIS, they pass a room in which monstrous forms like the Vortex Wraiths are being tended to by medical doctors, but they can’t stop to investigate; as it is, Morel and his guards still beat them back to the TARDIS. Morel demands that the Doctor open the door, but when he does so more Vortex Wraiths burst out of the TARDIS and attack the guards. The Doctor ushers his friends inside, including Jamon, reasoning that it can’t be any more dangerous than staying out here; and indeed, once inside they find that the TARDIS has somehow contrived to slaughter the Vortex Wraiths even as they attempted to tamper with its controls.

The Doctor determines that the damage to this region of space-time is more extensive than he’d thought, and theorises that it may have been caused by the widespread use of Transference. In this region, FTL velocities and time-travel are physically impossible, and the fact that the TARDIS is still working is putting a strain on the causality of its passengers’ existence. As a result they are occasionally behaving as they would have in the past, or will in the future. This may have something to do with the argument which breaks out between Anji and Jamon; when she can no longer stand his patronising attitude, she starts to ask him pointed questions about the nature of Transference, which call into question the most basic assumptions about his life. There’s no physical proof that the Soul exists; thus, perhaps the man who thinks himself to be Jamon is just a copy of a copy, programmed with false memories of a man who is long since dead. Jamon is so horrified that he slaps Anji in the face before he realises what he’s doing, which doesn’t improve their relationship.

The TARDIS has been damaged, both by the Vortex Wraiths’ incursion and by the strained nature of space-time in the Empire, and the Doctor therefore puts down on a nearby planet so the ship can rest and repair herself. It would be easier and safer to wait inside while it does so, but the Doctor nevertheless insists upon going out to explore. They have materialised in a jungle, where they meet the members of Professor Axon Miribilis’ travelling circus and are invited to share the warmth of the fire for the price of a story. Miribilis and his performers explain that this is the planet Thakrash; it was once part of the Empire until a star fell from the heavens and shattered the Transference Pylon. Once isolated from the rest of the Empire, the slaves revolted and overthrew their brutal rulers, but it is said that there is a Citadel very near here where the old ways continue...

In exchange for the circus’ hospitality, Anji tells the tale of the demon goddess Devi, and Fitz tells the tale of Sir Gawain and the Green Knight. Jamon tells the local version of the story of Siddharta, the tale of a legendary being known as the Healer of Worlds. Born to a mortal mother and immortal father, he found his way to his father’s realm after his mother’s death, and was sheltered from the frailties of mortal man so he could rule them as prophesied. However, the boy was more powerful than even his father dreamed, and when he ventured beyond his boundaries he learned that real men grow sick, get old, and die. He thus cast off all ties of family and power to roam the world of mortal men and learn the truth of it. In his travels he was beset by the demon Dominas, who tried every threat, lure and trick there was to cast him down; however, he overcame these obstacles and achieved Enlightenment. Rather than pass out of this world, however, the Healer of Worlds contrived to be reborn and continue his travels, to show others the truth of things. Legend has it that this being is an aspect of the Creator, or perhaps an echo of some future being who will save the Universe itself...

Now it’s the Doctor’s turn to tell a story, but before he can do so, he hears Anji screaming. She has wandered away from the fire to avoid Jamon, and has encountered a slimy, loathesome shape-shifting creature nearby. The Doctor’s erratic memory tosses up the name of the thing’s species; it is a Collector, one of a race of creatures who roam the Universe looking for nice shiny things and taking them. This particular Collector is a scout, who ventured into this area of space to look for new shiny things, and accidentally crashed into one, destroying the shiny thing and its ship. It hid out in the forest for centuries, alone, until it encountered Miribilis’ circus and found a way to put its shape-shifting abilities to use as an entertainer.

At this point, a mortally injured man stumbles into the clearing, clutching a shard of some crystal-like substance which he passes on to the Doctor. Hooded figures burst in after him, guided by animals like reptilian bloodhounds. The Doctor, realising that the circus folk can’t defend themselves, identifies himself as a powerful sorcerer and offers to exchange himself and the shard for the others’ safety. The hooded figures accept the offer, and Miriblis’ people refuse to intervene; the telling of stories is a sacred bond on this world, and as the Doctor did not do so, they are not bound to help him. Anji, Fitz and Jamon set off in pursuit of the hooded figures, accompanied by the Collector, who realises that the Doctor poses its best bet of getting off this world and back home to its Collection.

The Doctor is brought before the High Ambassador Elect, who recently murdered his predecessor to gain his title. The Order of Souls has tried to maintain the rites of their Ambassadorial ancestors, but over the centuries the rituals have become corrupted and meaningless. Although the Pylon, which shattered when the Collector’s ship crashed into it, has been painstakingly pieced back together over the centuries, the Doctor knows that it will never work properly in its current condition. Nevertheless, the Ambassador Elect has the Doctor chained up and stabs him in the chest with the recovered shard, using his blood as a conductive liquid to affix the shard to the rest of the Pylon. The Doctor’s friends arrive at the critical moment, and while Jamon fights off the members of the Order, Anji releases the injured Doctor. They all flee as the malfunctioning Pylon discharges galvanistic energy into the assembled members of the Order, and screaming faces bubble up on their skin before the Pylon explodes and kills them all.

The Doctor allows the Collector to take some of the Pylon’s remains so that nobody can try this stunt again, and manages to return to the TARDIS despite occasionally fainting from blood loss. Once back in the TARDIS, he heals himself and Jamon, who seems uncharacteristically diffident in mentioning that he too felt oddly affected by the sick energies from the Pylon; it’s as if there’s something on his mind he doesn’t want to share. Once he’s seen the Collector off to a shiny, pretty part of the TARDIS, the Doctor returns to the console room and generates a long-range view of the Empire. It appears that some force, somewhere in the Transference network, is exerting a malign influence upon the rest of the Empire, but the Doctor isn’t sure what or why. There seems to be an informational nexus on the planet Goronos, where data from the far-flung outposts of the Empire is collected, analysed and passed on. Perhaps there they will find more clues to the nature of the threat...

The TARDIS arrives on Goronos in an urban wasteland where flaking posters of the stern leader Uncle Chumley look over skyscrapers which have been untended for centuries. Fitz is beginning to believe that he and his friends are being manipulated, but before he can explain this they are attacked by an Ambassador named Jarel and an army of walking corpses, and are placed in the Cyberdyne, a virtual reality matrix in which the people of Goronos live out their lives. As a native of the Empire, Jamon is completely subsumed by the network, and perceives himself living a perfectly ordinary, mundane life as a data processor. But the network can’t cope with Fitz and Anji’s more complex desires, and their simulations break down. Fitz’s fantasy of being a world-famous rock star is regarded as evil and subversive in this world where nobody is meant to be the centre of attention; thus, although he gets all of the attention and concerts, it’s granted at the whim of his Master, and he gets none of the perks associated with the fantasy. Anji is an ordinary financial consultant, until one night she is attacked and pursued through the streets by a vicious, bald serial killer; fortunately, she is saved by a dapper man dressed in a business suit and carrying a silver cane, who unleashes a monstrous and unperceivable form upon the killer. He then talks her out of her fantasy, and she wakes to find the Doctor doing the same in the real world. Presumably the “killer” was her mind’s interpretation of Jarel, and the dapper man in the suit was her intepretation of the Doctor; yet later, when she thinks about it, she realises that the dapper man didn’t give the impression of being the Doctor at all. Perhaps he was someone else entirely...

The Doctor frees Fitz and Jamon, and Jamon in particular is horrified by what he’s gone through and refuses to discuss it. The Doctor reveals that while breaking free of the Cyberdyne he learned that Goronos was once ruled by a strict caste system; when the slaves overthrew their masters, the social structure collapsed, and as the slaves couldn’t imagine any other way of living they created a new kind of slavery for themselves. On the upper floor of the pyramid complex, they find the computers which correlate information from all corners of the Empire, and also the TARDIS, which Jarel has brought in for examination. Anji and Jamon work together to extract the data the Doctor needs to build up an overview of the Empire, and they depart in the TARDIS -- while Jarel waits for the Doctor’s curiosity to lead him into the trap.

Aboard the TARDIS, the Doctor determines that the Pylons were seeded from one particular world millions of years ago. Lobotomised prisoners were launched into space in search of inhabitable worlds; when they located one, they fulfilled their programming by setting up a Pylon and then dropping dead. Eventually the Empire became self-sustaining, but the process of interstellar Transference has warped space-time in the vicinity. Worse, the Empire appears to be falling apart; people are fighting wars or polluting their environments on almost every world. When the Doctor studies the Transference network with the new data in mind, he detects the anomaly he’s been looking for; rather than travelling directly from world to world, the Ambassadors are instead being diverted to one world in particular and then sent back out into the Empire. The Doctor suspects that this world is the real home of the Empire, and where the answers lie.

The Doctor travels to the world in question, where he takes Anji and Jamon out to investigate while leaving Fitz to keep an eye on the Collector. The planet turns out to be a devastated world of dust, and there, with no environmental distractions, Anji finally realises that the Doctor has been manipulating them all, forcing them out of the TARDIS on Thakrash and Goronos to draw attention and act as bait. He admits that this is true, and calls on his enemies to show themselves -- and when they do, they are revealed to be Vortex Wraiths, who long ago used the Pylons to generate bodies for themselves and destroy the population of this planet. Each Wraith is clutching the desiccated body of an Ambassador; when the Ambassadors arrive on this world, the Wraiths use the Pylons to transmat copies of their bodies elsewhere in the Empire without destroying the original. This enables them to control the Ambassadors by using their old bodies as virtual voodoo dolls, and through these puppets the Wraiths have been forcing the Empire into chaos, making it possible for more of their kind to cross into this reality. But this has been slow work, and now there is a new urgency involved, for there is something new in the Vortex -- something terrible which the Vortex Wraiths must escape at all costs...

The Wraiths order the Doctor to link his TARDIS to the Pylons and generate new bodies for them, which they were unable to do themselves due to the TARDIS’ defenses. When the Doctor refuses, the Wraiths reveal that they have a copy of Jamon, and try to force him to attack Anji. Jamon has been suffering from an identity crisis ever since Anji first cast doubt on the nature of Transference, and his time on Goronos has nearly convinced him that he indeed has no Soul; but just as he’s about to give in, the Doctor points out that if he didn’t have a soul the Wraiths wouldn’t be able to use it to control him. Jamon literally pulls himself together, causing the life to go out of his other form. Since the Wraiths haven’t attacked them directly, the Doctor concludes that they are too weak to do so, and probably lied about destroying this world; that the makers of the Empire destroyed themselves in a war and the Wraiths just took advantage of the situation. The Wraiths, however, remind him that they can still use their Ambassadors to slaughter millions throughout the Empire unless the Doctor gives in, and he apparently does so.