The reptilian natives of the planet Betrushia have been at war for decades, but at last the Ismetch and Cutch seem ready to negotiate a cease-fire. However, there is still a great deal of bitterness between the two sides, and the Ismetch General Hovv has apparently deserted rather than agree to a negotiated peace. Before any treaties can be signed, however, contact is lost with a number of Ismetch cities, including the capital, Porsim -- and the last message transmitted from Porsim appears to be a warning that the Keth have come, a reference to a legendary evil said to herald the end of the world. The war-weary Grek orders his subordinate Liso to return to Porsim to investigate, despite Liso’s desire to remain on the front lines and carry on the fight against their enemies. Meanwhile, their medical officer Maconsa studies the body of a man brought in from the front, and finds that the shrapnel in his body is not ammunition, but meteorite fragments…

The Doctor, Ace and Benny have spent a relaxing vacation on the human colony of Massatoris, but as the Doctor prepares to leave, Ace tells him that she wants to stay for a while, to spend some time alone. The Doctor and Benny thus go to the nearby Betrushia by themselves to observe its famous ring system, but materialise in the jungle on the border between enemy lines. The Doctor is captured by an Ismetch patrol, while Benny, lagging some distance behind him, is captured by the Cutch. Despite her evidently alien nature, the Cutch officer Imalgahite apparently concludes that she is an Ismetch spy and orders his men to execute her on the Ismetch side of the border so the enemy can find her body. As soon as they cross the border, however, the Cutch firing squad squad is killed by an Ismetch sniper named Ran, who takes Benny back to the Ismetch camp for interrogation. He refuses to tell her why he was so far out in the jungle in the first place -- and neither he nor Benny realise that Imalgahite had planted a homing device on her clothing, and is using her to locate the Ismetch dugout.

The Doctor is questioned by the curious Grek, and saves his life when a bombardment nearly brings down the dugout roof on his head. Intrigued by what he has learned so far, the Doctor slips away to investigate further, and when Grek discovers that the Doctor has escaped, he decides to send Benny with Liso in order to keep her under close guard and ensure the Doctor’s good behaviour. Liso considers the mission to Porsim pointless, and is even more furious to be saddled with guarding an alien as well -- but anger is dispelled by shock when his dirigibles arrive at Porsim, which has been levelled by some incredible force. The Ismetch dirigibles are then attacked by a giant black spaceship, and Liso and Benny retreat in an emergency glider, leaving the dirigibles to hold off their attacker while Liso reports to Grek. The dirigibles are no match for the ship’s firepower, however, and the ship forces them back towards the Ismetch dugout. Meanwhile, on the front lines, isolated soldiers and patrols are being attacked by a glutinous yellow ooze which bursts up out of the ground to consume them without warning…

The Doctor discovers that the Ismetch dugout was built atop an ancient temple. The old priest Thoss seems unsurprised when he arrives; in the forbidden, apocryphal texts of the Ismetch religion, it is said that strange mammals will appear at the end of the world, when the skies fall and the Keth return. The Doctor tries to pry the “Kethstones” out of the shrine to examine them more closely, but Ran arrives and catches him vandalising a holy artefact. As Ran takes him away to be executed, however, several soldiers are injured by another meteorite bombardment -- and when the Doctor shows Ran that the meteorite fragments are identical to the Kethstones, Ran agrees to accompany the Doctor back to his TARDIS to investigate further. Once there, the Doctor takes the opportunity to double-check certain readings he took when he first arrived, and learns that things are worse than he’d feared; there is an instability in the planet’s core, and within days Betrushia will be destroyed. He pilots the TARDIS into orbit and spacewalks out into the rings, where his suspicions are confirmed; the meteorites are fragments from the ring system, which is falling out of orbit. He learns why when a giant black spaceship scythes through the rings, firing a burning red energy beam which destroys all in its path. The Doctor is knocked senseless by the shockwave and is swept up aboard the ship as it passes by, and the TARDIS automatically returns to Betrushia, taking the shaken Ran with it.

Elsewhere, a bald young woman is being indoctrinated into the Chapter of Saint Anthony, a cult which believes pain and suffering is the path to spiritual purity. She appears to be progressing well, but is haunted by vague memories of her life before the Chapter, and by a sense that what the Chapter is doing is evil. Her immediate superior, the bitter and sadistic dwarf Parva de Hooch, realises that she is forgetting her vows and threatens to send her to Magna Yong for punishment, but the frightened and confused woman beats him off and retreats into the corridors of the seminary. She hides in the seminary’s reactor room at first, but must leave when Parva de Hooch turns off the sun for the night. Searching for somewhere else to hide, she finds an observation platform overlooking the chapel of St Anthony, where she watches in horror as terrified captives are fed into a blazing inferno which burns them alive while the watching penitents chant and flagellate themselves. Unable to bear it any longer, she cries out in anguish -- just as the Doctor is brought in by Parva de Hooch, who found him wandering the lower levels of the “seminary”. The Doctor instantly recognises the young woman as Ace…

Imalgahite and his men attack the Ismetch dugout, overpowering the unprepared soldiers, killing Maconsa and taking Grek prisoner. Thoss is also captured, but he is in shock, and claims that while fleeing from the battle he saw a mass of yellow ooze spilling out of the ground and consuming the bodies of the dead… and that within the ooze, he saw the face of the missing General Hovv. Imalgahite ignores his ravings at first, and demands to know what the Ismetch have done to his own capital city; however, he slowly comes to realise that both sides are genuinely experiencing the same problem. When Maconsa’s remains are found on the battlefield, stripped down to their bones and coated with ooze, Imalgahite and Grek realise that they are facing a common enemy. At that moment, Liso and Benny arrive just ahead of the black ship, which has herded the Ismetch dirigibles back to the dugout simply to destroy them before the Betrushians’ eyes as a demonstration of power. Meanwhile, Ran searches the forest for the one thing that has made his life worth living ever since his civilian lover died in a Cutch attack.

The Chapter’s mothership descends from orbit to join its shuttle by the Ismetch dugout, and Magna Yong sends out the Chaptermen to bring enlightenment to the Betrushians as painfully as possible. He decides to let the Doctor run free, as he hasn’t had a decent challenge in years and wants to see just how far the Doctor will get in opposing him. The Doctor thus questions Ace, who is beginning to reject the Chapter’s conditioning. She tells him that the Chapter attacked Massatoris soon after he left; most of the colonists were killed, but a selected few such as Ace were brainwashed and enslaved by the Chapter. Parva de Hooch then tries to kill them, as he disagrees with Magna Yong’s decision and believes that the Doctor poses a real threat. The Doctor and Ace overpower him and return to the Ismetch compound, where the Doctor believes he will find the answers to the puzzle of the ring system. Parva de Hooch blames Yong for this humiliation, but is unwilling -- for now -- to challenge his leader publicly. Meanwhile, the yellow ooze continues to rise, consuming errant Chaptermen as they progress further into the jungle -- and a yellow haze appears on the distant horizon…

Benny, Grek, Liso and Imalgahite join forces, intending to steal the Chapter’s mothership and use it to evacuate the surviving Betrushians from their doomed world. They overpower Parva de Hooch, but are themselves captured by Yong and his men. Parva de Hooch realises that Benny is known to the Doctor, and takes her for brainwashing while the Betrushians are taken to the auto-da-fé along with the last of the Massatorian colonists. But just as the last human prisoner is fed to the flames, the ship is rocked by an earth tremor, and the Betrushians take advantage of the distraction to overpower their guards. Benny also uses the opportunity to escape from Parva de Hooch, and helps the Betrushians to seize control of the bridge -- where the cause of the earthquake becomes apparent. On the viewscreen, the horrified Betrushians and Chaptermen see that the mysterious ooze is tearing itself free from beneath the surface of the planet and is rampaging through the jungle, devouring everything it encounters.

The Doctor and Ace return to the temple, where the Doctor forces the terrified Thoss to look at the samples he took from the rings, proof that they are artificial. Thoss reluctantly opens up a panel in the temple to reveal a relic of the Time Before, an artificial polygon constructed by a race which existed on the planet before the current species evolved. Inside, the Doctor finds a recorded message from an extinct mammalian species, and after viewing it he rushes back to the mothership with Ace to warn the Chaptermen of the danger. The yellow plasm is a genetic inhibitor, created by the original Betrushians to regulate the process of evolution, but it went out of control and consumed every living thing on the planet. In the little time remaining to them, its creators built a system of miniature satellites to confine the organism to their own world and thus protect the rest of the galaxy from their mistake. Once all life on the planet’s surface had been consumed, the regulator sank into dormancy and settled into the core of the planet, allowing life to evolve once again -- until the Chaptermen began to destroy the ring system which was keeping the organism confined. As the regulator tears itself free of Betrushia’s core, it is destroying the planet in the process -- and if nothing is done to stop it, it will rampage across the galaxy, destroying all life wherever it is found.

Thoss forces himself to enter the polygon and face the truth, but in his shock and desperation as his beliefs crumble about him he releases the Chaptermen, believing they have come to show him the way. The Chapter thus regains control of the ship, but Yong refuses to help destroy the organism, believing that it is a manifestation of the will of Saint Anthony. The others aren’t convinced, and de Hooch stages a coup and seizes control of the Chater; he still intends to avenge his humiliations on the Doctor, but agrees to help destroy the organism first. The energy from the auto-da-fé, Saint Anthony’s Fire, will be used to boost power to what remains of the ring system, keeping the organism confined to Betrushia until the planet breaks up completely and destroys it. Benny and Liso use the shuttle to pick up as many survivors as they can, and then take up position in the ring system and wait for the Doctor to act.

Yong escapes from his captors and tries to shut down the mothership’s reactor, but Ran is hiding there, protecting his lover’s clutch of eggs. Ran shoots and wounds Yong, who loses his protective goggles and is blinded by the light of the artificial sun. The Doctor instructs de Hooch to activate the directional controls in the chapel, but de Hooch instead sets off after Yong to avenge himself. Yong himself is heading for the temple to destroy the controls, and while there he kills both Thoss and de Hooch. Yong is himself immolated when the Doctor is forced to activate the Fire on schedule; but without the directional controls on line, the energy dissipates uselessly into space. Grek gives his life to enter the burning temple and activate the directional controls, focussing the Fire into the ring system as the Doctor had intended. The organism is thus safely contained on Betrushia.

The Doctor evacuates the Betrushians into the TARDIS, and leaves the Chapter to face the natural course of justice -- unaware that Benny and Ace have taken matters into their own hands by deactivating the mothership’s navigational controls. The Chaptermen thus remain trapped in orbit as Betrushia explodes, destroying both them and the regulator. The Doctor takes the surviving Betrushians to a new life on the now-abandoned Massatoris.