A new planet has entered the Rhumon star system, and both the Imperial and Republican factions have laid claim to it. Representatives of both factions are stranded on the new world after a brief battle disables both their ships, and they reluctantly settle into an uneasy truce while waiting for reinforcements to arrive. As time passes, however, it becomes clear to the commanders of both forces that their superiors do not intend to waste further resources on what was mainly a symbolic gesture to begin with. To make matters worse, the native life forms have not been entirely subjugated, and rumours are beginning to spread that the forests are being stalked by the ghosts of soldiers killed in battle. The Imperials' high priest, Father Modeenus, is enforcing severe penalties for such blasphemous talk, as is his opposite number, the Republicans' Morale and Discipline Officer, Nevon-two. It cannot be denied that bodies are vanishing from the battlefields, but both sides believe that either the natives or the opposing faction is responsible -- a belief which serves the purpose of the dark force lurking elsewhere on the planet...

The TARDIS materializes with difficulty on the disputed world, and the Doctor, Jamie and Victoria emerge to explore. They are captured by Republican soldiers near a native habitat in the cliffs, but Victoria escapes into the cave tunnels -- and the two soldiers sent in after her are attacked by shambling, grey monsters and killed. Commander Coroth, unwilling to remain in this dangerous area without reinforcements, decides to take the Doctor and Jamie back to his base for questioning -- but on the way they are attacked by Imperial troopers who take them all prisoner. Father Modeenus has the Doctor and Jamie placed in the "integral analyser" to determine their moral and spiritual purity, but is unable to make any sense of the readings it gives him. The Doctor scoffs at the suggestion that a machine could objectively analyse a subject's moral purity, but fortunately Lord Kai Shallvar arrives just in time to prevent the enraged Modeenus for executing the Doctor for blasphemy. Shallvar sends the Doctor and Jamie to the work yard along with the Republican prisoners and enslaved natives -- and when the Doctor recognizes the natives as Menoptera, he realizes that he has once again arrived on the planet Vortis during a crisis in its history.

Victoria flees from the grey creatures only to be captured by rebel Menoptera who intend to use her as a subject in their weapons tests. The Rhumon have calibrated their weapons to respond to the same factors registered by the integral analysers, thus ensuring that each side's weapons are effective only against the enemy. The Menopteran weapons have no effect on Victoria, who is not of Rhumon origin, and when they realize that she can speak their language and is a companion of the famous Doctor, they release her with abject apologies. They have also captured an Imperial engineer named Annolos and a Republican soldier named Torth, and hope to be able to tune the weapons to stun both sides of the conflict. Victoria, realizing that the Menoptera are fighting to reclaim their planet, agrees to help them, and the Menoptera in turn agree to help her rescue her friends. Since the Rhumon defenses do not affect Victoria, she will be able to pass through their defense fields, disguised as a Menoptera, and find and rescue Jamie and the Doctor. But as the Menoptera are unaware of the Imperial ambush, they assume that the Doctor and Jamie are prisoners of the Republicans, and send Victoria to the wrong base.

The Doctor and Jamie also discover that they can pass through the Rhumon force fields, and thus organise a break-out before the Imperials realize the significance of the readings from the integral analyser. Shallvar blames himself for not recognizing the danger in time, and takes out his frustration on Father Modeenus when the priest claims that the Doctor and Jamie are embodiments of evil. Modeenus, already concerned by the decline in his congregation's moral purity as shown by the integral analyser, worries that he has not been carrying out his duties properly -- and when he returns to the golden temple of Omnimon and prays for a sign, he unexpectedly receives one. Meanwhile, in the Republican camp, the fiercely dogmatic Nevon-two has taken to confiscating the captured medals of Imperial troops, claiming that such "trophies" inspire unworthy thoughts of competition and inequality. What nobody realizes is that in the privacy of her own quarters, she has been fondling the medals against her own skin, an act which gives her pleasure and seems to put her in communion with higher powers she believes to be the spirit of the Revolution.

After running out of slogans to shout at each other, Annolos and Torth have come to realize that the native resistance is more organised and advanced than they had ever dreamed possible. Knowing that they must warn their own people of the danger, they reluctantly work together, using spare parts to assemble a distress beacon which they attach to one of the Zarbi beasts wandering near their cells. The Rhumon will detect the signal when the Zarbi is released to the surface to feed, and Annolos and Torth agree to leave up to chance which side will do so first. Meanwhile, the Doctor and Jamie return to the caves to search for Victoria, with the help of the grateful Coroth and the elderly Menoptera Yostor, but upon arriving they are attacked by the grey, fungus-like creatures. They manage to escape, but in his haste Coroth crashes the escape vehicle into a grove of somnolos berries and is killed. The Doctor, Jamie and Yostor succumb to the berries' vapour and pass out, and by the time they recover, nearly a day has passed -- and Coroth's body has vanished.

Nevon-two is growing more intractable as morale declines, and Captain-Commander Draga-three decides to put an end to the rumours once and for all by exhuming the graveyard to show that there is no substance to the stories of ghosts. Unfortunately, the plan backfires when the graves prove to be empty. In the ensuing confusion, Victoria's disguise is penetrated, and Nevon immediately accuses her of being an Imperial spy. Draga agrees to fit Victoria with a shock collar to ensure her obedience, and to send her back to the Imperial base to spy for the Republicans -- but when as Victoria enters the base, Nevon begins to guide her towards Shallvar's quarters, and Draga's subordinate Relgo realizes that Nevon has fitted the shock collar with a bomb. When he attempts to stop her, the controls for the collar are damaged, convulsing Victoria with repeated shocks, and despite Nevon's protests Draga deactivates it to save Victoria's life.

The Doctor, Jamie and Yostor hide out in a Temple of Light while waiting for word of their escape to reach the rebel compound, and the Doctor takes the opportunity to question Yostor about his people's religious beliefs. Yostor claims to have seen the Gods of Light himself as a child, and the Doctor, while reserving judgement on the nature of the Gods, suspects that he may be close to answering a nagging question -- how can beings the size and shape of Menoptera possibly fly? Republican forces learn of the Doctor and Jamie's presence and attack the Temple, and whereas Jamie manages to escape with the help of the rebel Nallia, the Doctor is recaptured. Due to the cemetery incident and Victoria's capture, security at the Republican base has been increased, and it is thus impossible to rescue the Doctor at this time. Jamie is taken to the rebel base, where he offers advice on its defense and sees that the Menoptera are teaching their children fly in secret in the hope that they will be able to escape from the Rhumon-occupied sectors of their world. When Jamie sees the angry Annolos and Torth shouting at their captors, he brings a group of children to face them and demands that they justify their invasion of the Menoptera's planet to the faces of their victims. To their shame, they find they are unable to do so.

The Imperial forces pick up Annolos and Torth's signal and locate the rebel base, and Shallvar decides to lead the assault personally. Jamie helps the Menoptera to hold off the attackers, and the Menoptera free their captives to fend for themselves. But in the thick of the fighting Annolos is unable to get to safety, and when he and Torth realize that children are being killed in the assault, they remain to help their former captors to escape. Shallvar's troops successfully seize control of the stronghold, but when Shallvar finds the bodies of the children he realizes to his horror why the Menoptera were fighting so fiercely. Meanwhile, Jamie and his allies seek shelter in a cleft in the cliffs, but before they can decide what to do with Annolos and Torth, they find that the cleft opens up into a canyon filled with battle tanks from both sides of the conflict -- and with fungal pods, which, as they watch, split open to reveal duplicates of the Rhumon soldiers killed in battle. The duplicates pursue the intruders into the caves, and Torth blows up the tunnel behind them to prevent any further pursuit -- leaving them with no choice but to go on, towards whatever else may be lurking in the tunnels. As they pass through a deserted Menoptera settlement, however, they see the duplicates mining the tunnels, and they are separated from Nallia, who escapes from the tunnels as the entrances explode and collapse behind her.

While the Doctor is being questioned by Draga, Victoria returns, claiming that the kind Father Modeenus gave her food and helped her to escape. The Doctor, however, suspicious of Modeenus' motives, examines her closely, to find that Modeenus has fitted a voice-activation system to the bomb, set to detonate when it detects Draga's voice. The Doctor defuses the bomb, but Nevon then demands that Victoria be placed in the integral analyser -- which seems to indicate that she has taken on the morality of the Imperial forces. The Doctor finally realizes what is really happening, and when he confiscates the rations given to Victoria by Modeenus and has Victoria go through the analyser again, the readings are completely different. This machine does not and never has detected moral or spiritual purity -- rather, it responds to the trace minerals in the Rhumon diet, and the difference between the Imperial and Republican diets has been misinterpreted by unscrupulous scientists and used for political purposes.

The Doctor returns to the Imperial base to reveal the truth to Shallvar, but before he can do anything about it, the duplicates enter the base and seize control -- with the aid of Father Modeenus, who believes that they have been restored to life by the grace of Omnimon. The Republican base falls to Nevon-two, who believes the duplicates to be embodiments of the super-state's superiority over the individual. The captive Rhumons are put to work digging for the mineral isocryte, and are then forced to board transports taking the isocryte to the sea coast. There, Modeenus and Nevon realize that the duplicates are not under their control after all, and are taken prisoner as well. The transports carry their captives to an offshore island, where they are all confronted by a hideous fungal creature -- a seed of the Animus which survived its previous encounter with the Doctor. It has been biding its time, preparing to take Vortis by stealth, but has had to move slowly due to the Menopteran ccustom of burning the bodies of the dead; the war has allowed it to accelerate its plan, however, as the Rhumon bury their dead, giving the Animus access to a suitable slave force. Modeenus was brought under its control by the concentration of gold in his temple, while Nevon fell victim to the gold in her confiscated medals. The Animus absorbs Nevon but rejects Modeenus, who has been driven mad by the duplicates' betrayal and is therefore no longer suitable for absorption.

The Animus' captives are put to work pouring their isocryte into the acid pools which supply the Animus with mineral nourishment, and the Animus absorbs the isocryte directly into its body; soon it will have the weapon it requires, and within a day it will have covered the planet. Just as it is about to absorb its captives, however, the Menoptera arrive with a fleet of spacecraft which they have been preparing in secret. Jamie and his allies also arrive and join the fight, enabling the Animus' captives to escape. The Animus, however, is rapidly learning to control the new powers granted it by the isocryte, and it is thus able to deflect energy beams from the Menopteran ships and draw the ships towards itself. The Rhumon and Menoptera barely escape with their lives, and as the Animus' new web begins to grow across Vortis they realize that they must put aside their difference to fight their common foe. Modeenus is amongst the survivors, and he vows to help put an end to the evil force which had so deceived him.

An emergency war council is convened, at which the Doctor explains the properties of isocryte and thus the extent of the danger they now face. Electrical stimulation causes isocryte to produce counter-gravitational waves; thus the Menoptera are able to fly because the trace elements of isocryte in their diet are absorbed into their nervous system. With the power of isocryte at its disposal, the Animus will soon be able to divert the course of Vortis itself and attack the other worlds in the Rhumon system. As it is now, the Animus can deflect any missiles launched at it, but the Doctor has a plan; believing that the turbulent materialisation of the TARDIS was caused by the concentration of isocryte on the planet's surface, he concludes that if he disengages the time drive he can pilot the TARDIS to the heart of the turbulence and thus carry an armed warhead to the Animus itself. He is accompanied by Jamie, Draga, Shallvar, the penitent Modeenus and a Menoptera named Kristas -- but instead of materializing on the Animus' island, the TARDIS arrives in a vast chamber filled with alien machinery and the preserved bodies of native life forms. A vast, glowing gaseous entity appears and begins to operate the machinery, and although Kristas believes it to be one of the Gods of Light, it apparently panics and flees through a hyperspace bridge when the Doctor tries to communicate with it. The Doctor now knows the truth; Vortis is a hollow, artificial world created by a race of plasma beings who appear to have been conducting some sort of scientific experiment.

The Doctor sets to work on the alien machinery, which is used to maintain the artificial world's biosphere as it travels through space, and soon works out how to trigger volcanic eruptions. His attempt to destroy the Animus backfires, however, when the Animus, driven by necessity, uses the isocryte in its body to lift itself up off the island and fly across the world, now impervious to attack. Meanwhile, an offshoot tentacle from the web pushes its way through the tunnels found by Jamie and the others, and emerges in the highlands, forcing the Menoptera to fight on two fronts. Annolos and Torth are killed trying to sever the tentacle, and Victoria and Nallia are forced to flee from the pursuing web. Meanwhile, more Gods of Light emerge from the hyperspace bridge, including one which is much larger than the others. This one allows the Doctor to communicate with it, and reveals itself to be a teacher who has stumbled across an illicit experiment being conducted by two of its young students. The experiment is Vortis, and it has been contaminated by another, jealous student using a sample of forbidden organic matter which he had stolen from his teachers.

Aware of the threat posed by the Animus, the teacher emerges onto the surface of Vortis to do battle, but it is defeated and is forced to retreat. The Animus then extrudes portions of itself into the heart of Vortis to seek out and destroy its new enemies, but the Doctor discovers that the communications unit is capable of projecting images with tactile force, which is how the students manifested themselves to the Menoptera while monitoring the progress of their experiment. He thus projects giant images of his companions to the surface of the planet, giving them just enough tactile energy to tear the Animus to shreds. The teacher and his fellow plasma beings then replenish Vortis with enough energy to maintain its stable biosphere, and promise to leave the Menoptera alone from now on. As the Doctor prepares to depart, however, Modeenus locks himself in the control chamber and attempts to cleanse Vortis of evil by piloting it into the sun; however, one last shred of the Animus, still carrying the remnants of Nevon-two's personality, slips through a crack and attacks Modeenus, and while he is distracted the Doctor reluctantly operates a flash-sterilisation procedure, incinerating both Modeenus and the Animus fragment. He then pilots Vortis into a stable orbit around the Rhumon sun. The crisis averted, Shallvar and Draga agree to give the Menoptera their freedom and make Vortis a neutral ground, and the Doctor and his companions depart in the hope that the Rhumon at large will learn from the example of their representatives on Vortis, and settle their differences in peace.