In a nameless city where the pursuit of science has been outlawed, Grand Knight Himesor of the Knights of Kuabris has reluctantly allowed some limited experimentation to improve the lot of the people. This has resulted in the creation of the Furnace, a primitive power station which supplies only the richest households with electric power. The people, having had a glimpse of what science can offer them, are now demanding more, and to make matters worse, ape-like creatures are emerging from the impassably toxic sewers to attack the people of the city. Oiquaquil, captain of the City Guard, is unable to contain the attacking creatures, and Himesor fears that the underground Brotherhood of Rexulon is spreading rumours that the ape things are from the legendary Menagerie of Ukkazaal, where men who meddled in science were turned to beasts. If the attacks come to be seen as divine punishment for the creation of the Furnace, the Knights may be overthrown and the Brotherhood will impose an even more tyrannical rule upon the city.

Seeking a way to penetrate the sewers, Himesor summons the mage Defrabax to answer claims that he has constructed a homunculus. Defrabax denies the rumours, and Himesor releases him, but orders his second-in-command Zaitabor and the loyal Knight Araboam keep an eye on him. Meanwhile, Defrabax’s apprentice Cosmae takes advantage of his master’s absence to summon the young prostitute Kaquaan, with whom he has fallen in love. Afterwards, Kaquaan leaves the sleeping Cosmae and steals what appears to be a gemstone from the mage’s table, but she is then frightened out of the house by the arrival of the homunculus. When Defrabax returns he sends the homunculus away so the knights won’t find it, but then finds that the gemstone, a vital part of his plan, is missing. Realising what has happened, he orders Cosmae to retrieve it. Cosmae leaves the house, but finds that Kaquaan has run right into Araboam, who has sent her to the castle of the Knights for questioning.

The TARDIS materialises in the city, and the Doctor and his companions emerge to explore. Unfortunately, the pub they choose to enter is unlicensed, and is raided by the Knights. Jamie escapes, but the Doctor identifies himself to the guards as a scientist and is sent to Himesor for interrogation. When the Doctor claims to fight evil, Himesor orders him to lend his expertise to the problem of the Menagerie. After hearing the legend, the Doctor plays a hunch and asks to see the Knights’ most holy artefacts from the previous age. As he had suspected, they are all technological items whose purpose has been forgotten; and what’s more relevant, the ancient “armour” of the Knights in fact possesses self-contained breathing units, which can be used to penetrate the noxious sewers and the Menagerie beyond. Himesor plans to lead an expedition into the Menagerie, leaving Zaitabor to lead in his absence -- although Zaitabor is furious with him for showing their ancient secrets to the Doctor.

Zoe is unable to pay her fine and is thus sent to the slave market. There, she is purchased by Diseada, the owner of a circus and freak show outside the city. At the circus, Zoe meets the conjoined twins Raitak and Reisak, who assure her that Diseada is not a cruel master and show her about her new home. Zoe becomes concerned about one of Diseada’s other purchases, a casket containing a dangerous-looking creature which appears to be all muscle, tooth and claw. The casket is in fact an ancient cryogenic unit, which has only recently run out of power. Diseada, concerned with getting the show up on time, dismisses Zoe’s warning that the creature could still be alive… Meanwhile, back in the city, Jamie finds Cosmae also seeking a way into the Knights’ castle, and they join forces to convince the guards that they’re a prisoner and escort. The guards pretend to fall for the old trick, but send word ahead to Zaitabor to expect the new arrivals…

The ape creatures, Rocarbies, are in fact working for Defrabax, who intends to stir up public feeling against the Knights and start a revolution. Defrabax wants new rulers who will sanction scientific experimentation, and he has promised the Rocarbies that if they help, the new rulers of the city will allow them to emerge from the sewers and live on the surface. The Rocarbies are growing impatient, however, and though Defrabax has not yet found the missing key, he must proceed to the next stage of his plan. The Knights’ expedition to the Menagerie, meanwhile, passes through the toxic regions of the sewers and into the underground remains of an even more ancient civilisation. There, they are attacked by giant moth-like creatures, and only a single knight escapes, taking word back to the Knights that Himesor is dead. Zaitabor thus becomes the Acting Grand Knight.

Jamie and Cosmae see Zaitabor moving through the corridors, and follow him to a secret panel behind a tapestry and thence to a chamber where the Brotherhood of Rexulon has assembled. There, they intervene to prevent a hooded Brother from sacrificing Kaquaan, but realise too late that they’ve been led into a trap. They are both gassed and left to recover in the castle, where Araboam captures them. He apparently refuses to believe their story, and they find that there is no longer a secret panel behind the tapestry. Araboam has Jamie and Cosmae locked up, but takes Kaquaan back to his own quarters -- where she surprises him, knocks him out, and rescues Jamie from the cells. However, there is no sign of Cosmae. Meanwhile, Defrabax delivers an ultimatum to the castle, threatening to destroy the Furnace and thus start a revolution unless they sanction further experiments. Zaitabor orders the Knights to find and kill him -- and then secretly communicates with one of the moth creatures from the Menagerie, giving it further instructions…

The moth creatures’ venom kills Himesor and his fellow Knights, but the Doctor survives. The moths take him through the underground city, past an ancient power station which is now blazing with light, and to their larder. There, they cocoon him and leave him for later consumption, but he is rescued by an intelligent shrew-like creature called a Dugraq, who confirms his suspicions that the Menagerie is all that remains of an ancient military research centre and that the creatures which live here now were either the subjects of experimentation or the results of genetic engineering. The Dugraqs attempt to keep the peace between the rambunctious Rocarbies and the moth-like Taculbain, whom the Rocarbies worship as gods. However, a surface-dweller recently captured the Taculbain Queen, destabilising the balance of power in the Menagerie. While seeking to warn the surface, the Dugraqs came into contact with Defrabax and gave him control of the research centre’s android so he could help search for the Queen. However, he has betrayed them, and is using the Rocarbies and the android to further his own agenda. Now the Rocarbies are nearly out of control, and without the android the Dugraqs have no way of keeping an eye on an even greater danger -- the sleeping Mecrim, which are evil personified…

Zoe helps out behind the scenes at the circus, but the show is interrupted when the creature from the cabinet awakens and begins slaughtering everyone it encounters. Zoe deduces from its behaviour that it is following sources of heat, such as those given off by living things, and she, Diseada, and the twins thus use the largest animal in the circus, the savannah walker, to lure the monster to the local village’s power station. The heat confuses it temporarily, but it soon learns to distinguish between the heat signature of the furnaces and those of living beings. As it attacks Zoe, however, Diseada gives his life to force it into one of the furnaces. With Disaeada’s death the ownership of the circus is passed on to his former slaves, but Reisak and Reitak agree to return to the city with Zoe to help find her friends -- and to find out where the creature came from, and if there are any more like it.

Defrabax orders the Rocarbies to destroy the Furnace and sends the android to activate the Menagerie’s power station, intending to supply unlimited power to all the people of the city. The Doctor and the Dugraq investigate the activity at the power station, and are just in time to stop the android from causing a catastrophic overload. The “gemstone” which Kaquaan had stolen was the key to the reactor’s test room, and Defrabax had decided to push ahead without waiting to confirm whether the reactor was safe; however, the Doctor is able to break into the test room, and he proves to the android that activating the ancient reactor now will destroy both the Menagerie and the city above it. The android contacts Defrabax, who is horrified by the revelation and accepts that he was wrong to betray the Dugraq. He apologises to the Dugraq and orders the android to obey the Doctor from now on. The Doctor and the Dugraq leave the Menagerie to discuss the situation with Defrabax, only to see a cloud of Taculbain flying out of the Menagerie and into a secret tunnel beneath the castle of the Knights. While the Doctor and Defrabax were distracted by their own agendas, something else has been going on behind their backs…

Kaquaan recognises Jamie’s description of the man who nearly killed her as Argaabil, a worker at the Furnace. She and Jamie confront him and force him to admit that the Brotherhood has taken Cosmae, but they are distracted when the Rocarbies blow up the Furnace on Defrabax’s orders. Argaabil escapes and tells Zaitabor what has happened, and Zaitabor kills him for betraying the Brotherhood. Jamie and Kaquaan, meanwhile, return to the castle and find that the tapestries have been moved about; the secret panel is still there, but behind a different tapestry. They enter the sacrificial chamber just in time to see Zaitabor returning the Taculbain Queen to her people -- in exchange for their having carried out his earlier instructions. The Mecrim are waking…

The City Guard arrives in pursuit of the Taculbain just in time to hear what has happened, and Oiquaquil arrests the assembled Brothers -- who are also horrified by what Zaitabor has done and agree to lend their support to the defense of the city. Jamie attacks Zaitabor, only to find that he has left a clockwork replica in his place as a distraction; but how could a man who hates science so much know how to build such a thing? Zoe and the twins arrive and tell their story to the Doctor, who realises that the creature they faced must have been a Mecrim -- just one, which killed hundreds of people in a single spree. And there may be any number of them in the Menagerie. The Doctor orders the android to keep an eye on Zaitabor -- after it has completed another task in the Menagerie for him.

Cosmae returns home to recuperate, while Kaquaan searches for Araboam, hoping that he can lead them to Zaitabor. She realises too late that Zaitabor and Araboam have gone to Defrabax’s home to seek revenge. They have captured Cosmae, but when Kaquaan tries to follow them the android, who has been watching Zaitabor as ordered, stops her from doing so and thus placing her own life in danger. Zaitabor, meanwhile, deduces that Defrabax must have destroyed the Furnace in order to replace it with another power source from the Menagerie; as he has not done so, this implies that it poses some danger, and Zaitabor therefore decides to complete his work. Meanwhile, the Taculbain find that it is too late to repair the damage they have caused; the Mecrim are awakening. Defrabax, Jamie and the Dugraq attempt to convince the Rocarbies to help fight the Mecrim, but the Rocarbies are no longer willing to listen to Defrabax and are about to kill him when the Taculbain arrive. The Rocarbies, who still believe the Taculbain to be gods, agree to fight alongside them.

The Doctor takes Zoe and the twins to the military centre, only to find that the Mecrim have already woken and escaped from their cryogenic units. The Doctor shuts the bulkheads between them, and while the Mecrim try to claw their way through, Zoe searches the ancient computer systems, trying to find a possible weakness. She learns that the Mecrim were engineered as weapons; however, a microbe in their intestinal tracts proved to be a contagious organism which wiped out the entire research team. The Doctor notices a familiar face in a photograph; this is the project’s government observer, who was cured of the plague through the use of cybernetic implants, exacerbating his obsession with the success of the weapons project. The Doctor confirms Zoe’s observation that the Mecrim track targets by heat signatures, and, concluding that they use the same method to recognise one of their own kind, he modifies the shelter’s explosive weapons to give off heat instead of exploding. When the Mecrim finally break in, he shoots one of his attackers with a heated bullet, changing its heat signature and causing the other Mecrim to turn on it. The Doctor, Zoe and the twins escape and take the weapon to Jamie. The other creatures of the Menagerie have suffered heavy losses in their battle with the Mecrim, but once Jamie starts firing the new weapon the Mecrim turn on each other.

The android follows Zaitabor to the power station, but as he holds Cosmae hostage and the Doctor has ordered the android not to take any life, it is unable to stop him from reactivating the reactor. Zaitabor contacts the Doctor and announces his intention to cleanse the city of evil and corruption, but the Doctor now knows who he really is -- the original project’s government observer, who tried and failed to escape in a shuttle when the planet was placed under quarantine. The crash wiped his cybernetically enhanced memory, and when he awoke, centuries later, he retained only a vague impression that scientific research led to destruction and was thus evil. The Doctor is unable to reason with him, and therefore takes the heat gun from Jamie and uses it to lure the surviving Mecrim into the power station. There, the Mecrim attack Zaitabor just as he activates the reactor -- unaware that the Doctor had already ordered the android to rig explosives which would destroy the reactor should anybody try to reactivate it. The resulting explosion destroys the reactor, and kills Zaitabor and the Mecrim -- and Cosmae.

The Doctor runs tests on Jamie and Zoe to ensure that they have not fallen victim to the Mecrim gut plague. Defrabax, blaming himself for Cosmae’s death, vows to atone for his actions by helping Oiquaquil to negotiate with the Rocarbies and Dugraq, enabling them to emerge from the Menagerie at last and live on equal terms with the surface dwellers. Kaquaan and the twins agree to help him do so. The Doctor and his companions depart, leaving the city with some hope for a better future.