The TARDIS materializes in the Prion Planetary System while the Doctor and Romana repair K9. The system contains two viable planets: Zolfa-Thura, a trackless desert in which the only remains of the civilisation which once flourished there are the mysterious five metal Screens; and Tigella, home of a humanoid civilisation which retreated underground to escape the carnivorous vegetation on its surface. The Doctor contacts the leader of Tigella, his old friend Zastor, to let him know that he's in the vicinity. Zastor is grateful to receive word from him, as his civilisation is facing a crisis; Tigella's survival depends upon power from the mysterious Dodecahedron, but in recent months the power has begun to fluctuate and the Tigellans cannot agree on a course of action.

There are two major camps amongst the Tigellans: the Savants, led by Deedrix, who believe that the Dodecahedron is a technological artefact to be studied and understood; and the Deons, led by high priestess Lexa, who believe that the Dodecahedron is a gift from the god Ti, to be worshipped. Deedrix accuses Lexa of conducting human sacrifices, as was once the custom of the Deons, and Lexa refuses to let the Savants examine the Dodecahedron, claiming that their blasphemy angers the god. In the midst of the arguments, the Savant Caris continues to advocate that the Tigellans should abandon their underground city and reclaim the surface. Zastor, unable to reconcile the opposing camps, calls on the Doctor to mediate -- but neither Deedrix nor Lexa trusts the motives of an alien and both feel that Zastor is abdicating his responsibility.

Meanwhile, somebody hires a band of space pirates, the Gaztaks, to kidnap an ordinary Earth male and bring him to the Screens of Zolfa-Thura. They do so, and General Grugger and Lieutenant Brotadac watch in astonishment as a huge building rises from the sands between the Screens. Inside the building they find a technologically advanced laboratory and a cactus -- which greets them by name. Meglos, the last Zolfa-Thuran, thanks them for bringing the Earthling and offers them a new business proposition; help him steal the Dodecahedron from Tigella. The Dodecahedron was manufactured on Zolfa-Thura, and its current power fluctuations are part of its original programming; once the changes are complete, its output will be enough to power an entire galaxy.

Grugger is sceptical, but eventually agrees to help. The Gaztaks place Meglos and the Earthman in a pair of cubicles against the wall of the laboratory, but Grugger then tries to leave them trapped while his men loot the laboratory. Meglos was expecting this, however, and Grugger and Brotadac find that they're now trapped in the laboratory; Meglos will not unseal the doors until they agree to obey him. Grugger thus completes the process, using the equipment in the laboratory to transfer

Meglos' mind and part of his physical being into the Earthman and thus giving Meglos a mobile humanoid host. Meglos has intercepted messages between the Doctor and Zastor, and has come up with a plan to penetrate the Tigellan city; but first he must deal with the Doctor...

The Doctor and Romana try everything they can think of, but are unable to break free of the chronic hysteresis. K9 can't help, as there is no known technological procedure for breaking such a loop. But a chance remark of Romana's inspires the Doctor, who suggests repeating their actions deliberately in order to create an interference pattern and shift the hysteresis out of phase. Despite the Doctor nearly forgetting his lines, this works, and the chronic hysteresis collapses, setting the Doctor and Romana free.

Brotadac admires Meglos' genius and the Doctor's coat, but Grugger is becoming irritated by Meglos' condescension and arrogance. The Gaztak ship lands in the jungles of Tigella, and Meglos sets off for the city, informing Grugger that he'll be back in one hour. He is greeted by Caris, who takes him to central control. There, he demands to be given access to the power room, but Lexa refuses to do so unless he agrees to take the Deon oath and swear allegiance to the god Ti. Meglos manages to control his fury and claims that he'd be honoured to do so. Once the oath is complete he demands that he be allowed to enter the power room alone, as it will be necessary to increase the violence of the baryon emissions -- a very dangerous operation. Lexa refuses, but Meglos points out that as he's taken the oath he is now under the protection of Ti. Lexa is trapped by her own demands and has no choice but to concede. Meglos enters the power room alone, and connects a small device to the Dodecahedron. Ten thousand years of waiting are about to be fulfilled...

The TARDIS misses the city completely, materializing in the jungle some distance away. As the Doctor, Romana and K9 approach the city, they find a strip of burnt vegetation, and Romana, curious, follows the path to find out what caused the burning. The Doctor continues on to the city before realizing that she's gone, and sends K9 back to fetch her. As the two confused guards watch the Doctor enter the city for the second time that day, K9 returns to the jungle -- but his batteries soon exhaust and he is forced to set off back to the city to recharge.

Caris enters the chambers outside the power room, intending to see what the Doctor's up to, only to find Lexa already there for the same reason. Before either can do anything about the other, they hear the Doctor returning, and they both hide and watch as the Doctor departs the power room without letting anyone know. Caris notices that the light from the power room has gone out, and she and Lexa enter -- and discover that the Dodecahedron is missing. They immediately report to Zastor, and Deedrix checks the power levels and finds that nothing more is coming through; the Dodecahedron is completely gone. Lexa demands that the Doctor be found and arrested, and moments later the real Doctor is captured while trying to find his way to central control. Meglos, meanwhile, hides from patrolling guards in the corridors of the city, and the stress of his situation causes cactoid features to break out on his skin.

At the last moment Grugger emerges from the ship and demands to know what's going on. Romana claims to have landed on the planet by accident and offers to show the way to her ship. Brotadac suggests waiting for Meglos to return, but Grugger decides to reassert his authority as leader and orders Romana to lead them to her ship. She tries leading them in circles for a while until they wise up, and then leads them to the clump of carnivorous plants which attacked her earlier. She flees back to the city while they're struggling to free themselves from the plants.

Tensions are growing back in the city as the power begins to run out. Ice is forming in the sub-corridors and even the most essential services are going dead. The Savants blame the Deons for preventing a detailed scientific investigation of the Dodecahedron; the Deons blame the Savants for angering the god with their blasphemy. Zastor, Lexa and Deedrix question the Doctor, who has no idea why they're accusing him of taking the Dodecahedron and suggests that they may all have been tricked by a doppelganger. Lexa insists that the Doctor be placed under arrest, but Zastor refuses and instead agrees to take the Doctor to the Power Room to investigate further. Lexa prepares to make her own arrangements...

Meglos hides in the corridors of the city, struggling to maintain his form as the Earthman tries to take advantage of Meglos' distraction to break free. Caris passes nearby, conducting maintenance on the failing systems, and Meglos takes her hostage and demands to be taken back to the surface. She refuses to do so until he shows her the impossible object he's carrying in his pocket -- proof positive that he is Meglos, the last Zolfa-Thuran, and that nothing is beyond his powers. Meanwhile, Lexa stages a religious coup, and the Deons begin to collect Savants and expel them to the surface. Deedrix and Zastor are arrested in the Power Room, but the Doctor is kept there -- to be prepared for sacrifice.

Romana stumbles across K9 near the city entrance and carries him in with her, while the Gaztaks break free of the attacking plants and pursue her angrily. Just as she passes the outer doors, the Deons seal off the city and she is trapped within the inner and outer doors. The Gaztaks attack the city's outer doors, and when they begin to break through the city guards mobilise, open the inner doors and attempt to fight the attackers off. Romana manages to get clear with K9, and as the battle rages she searches for somewhere to recharge him.

As Meglos searches for an alternative route out of the city, the Earthman tries once more to break free of his control. Caris takes advantage of Meglos' distraction to take him prisoner, using her laser cutter as a weapon. But Romana happens across them, and assumes that Caris is holding the Doctor at gunpoint. Romana surprises and overpowers Caris, and is subsequently surprised when the Doctor walks right past her and joins the Gaztaks outside. Caris recovers and explains who he really was, too late to stop him. The Gaztaks have defeated the city guards but found no loot worth taking, and Grugger blames Meglos for the total failure of their attack... until Meglos produces the miniaturised Dodecahedron from his pocket. They have their prize, and this is only the beginning. Meglos and the Gaztaks return to the Gaztak ship and prepare to take off.

Caris and Romana find a group of Deons taking Deedrix and Zastor to the surface, and warn them of the Gaztak attack. As the Deons head for the city gate, Romana and the Tigellans rush to save the Doctor, arriving just in time. Lexa demands that the heretics be removed, but a guard arrives from the city gate to announce that the Gaztaks have been driven off and that the Doctor has fled with them. Lexa realizes that the Doctor was telling the truth all along and releases him. The Doctor and Romana conclude that Meglos must be taking the Dodecahedron back to the Screens of Zolfa-Thura, the only artefact remaining on the planet, and set off with Deedrix and Caris to stop him. But as they pass the city gates, a dying Gaztak attempts to shoot Romana -- and Lexa is hit by the bolt and killed while pushing Romana out of the way.

Meglos and the Gaztaks return to Zolfa-Thura, while Grugger complains about the loss of three men on Tigella -- half his crew. But Meglos assures him that the Dodecahedron is approaching its full potential and was well worth the sacrifice. The Gaztak ship lands and Meglos buries the Dodecahedron in the precise middle of the space between the Screens, and then uses the Re-dimensioner to restore it to full size atop the laboratory building. His fellow Zolfa-Thurans fought themselves to extinction in a war over the use of the Dodecahedron as a weapon; now Meglos can fulfil his dreams and use the Screens to focus the energy from the Dodecahedron on any planet in the galaxy, blasting it to dust. Grugger insists that they test it out on Tigella.

Meglos sets the co-ordinates of the weapon and goes out to double-check the alignment of the Screens. The TARDIS materializes nearby, and while Meglos is outside, the Doctor pops into the laboratory, claiming to be him, and re-sets the co-ordinates. He tells the suspicious Grugger that he's just making sure everything is all right, and goes out for a walk to catch up with himself. Once he's departed, Grugger orders Brotadac to have him thrown into the security cell on the ship; they don't need him to work the weapon for themselves. Grugger offers to give Brotadac Meglos' coat once he's imprisoned, and Brotadac enthusiastically sends out two guards after him. The Doctor hides nearby and sees the guards overpower Meglos and drag him to the Gaztak ship; but when he emerges from hiding he runs into Brotadac almost immediately, and Brotadac drags him to the ship and throws him in the security cell himself without bothering to look inside first.

Romana and the others see the Doctor being taken on board the ship, and with K9's help, they overpower the guard and burn through the door of the security cell. The Doctor has just admitted to Meglos that he's altered the weapon's settings; if Grugger activates it now he'll destroy Zolfa-Thura. Romana and the others enter the cell, but when Deedrix and Caris try to restrain Meglos he disassociates his physical self from the Earthman and flashes out of the ship on a modulated wavelength of light. The Doctor and his allies flee back to the TARDIS as Meglos returns to his cactus body and tries to warn Grugger of the danger. The TARDIS dematerializes just as Brotadac, trying to abort the countdown, presses the wrong button and destroys the entire planet.