The TARDIS emerges into N-Space near the Metulla Orionsis system and the homeworld of the Traken Union, a society so tranquil that evil calcifies and dies within its rarefied atmosphere. The Doctor is surprised to find the TARDIS heading for Traken, but all is explained when an elderly man in a sedan chair materializes in the console room; this is the Keeper of Traken, and he has taken control of the TARDIS to ask the Doctor for help. The Keeper uses the TARDIS scanner to show images of his world, including the arrival of a "Melkur" -- a creature with evil intentions which froze in place the moment it touched down on Traken and never moved again. Young Kassia was placed in charge of its care and fulfilled her duties admirably, although the creature survived much longer than anybody had anticipated. These events took place years ago; now Kassia has grown up, become a Consul of Traken, and married her fellow Consul Tremas. On their wedding night, the Keeper released Kassia from her extended service to the Melkur and placed it in the care of Nyssa, Tremas' daughter from a previous marriage. He also named Tremas as his successor, for his thousand-year reign as the Keeper was nearly at an end. But as he did so he sensed some terrible evil being nurtured in the hearts of the three good people before him... As he no longer longer has the strength to defend his world, he needs outside assistance, and the Doctor gladly agrees to help.

As Consuls and citizens depart Tremas and Kassia's wedding, Kassia goes to the grove, ostensibly to bid farewell to Melkur. In fact she pours out her heart to the creature; although everybody believes the Keeper has greatly honoured Tremas by naming him Keeper-Nominate, Kassia only sees that when the Keeper dies -- which will be soon -- her new husband will be taken from her. She tells her fears to the silent, unmoving Melkur, as she doesn't know who else to confide in. But she isn't expecting Melkur to speak back to her...

The next morning, the body of an elderly Foster is found near the Grove, with an expression of terror on his face. Tremas, an amateur scientist, studies the body and determines that the man died through contact with some powerful energy source. Consul Seron listens gravely to Tremas' conclusions, telling the worried Luvic that he's just humouring Tremas -- although he may just be trying to soothe the frightened Luvic. In any case, the death has caused consternation amongst the ordinary people; as the Keepership nears its end, superstition and fears are bound to spread throughout the Union. Kassia, unwilling to reveal what happened to her in the Grove, insists that the Fosters be armed to keep order, and despite some reservations the Consuls agree to take this step.

Kassia orders the Fosters to kill the Doctor and Adric, but the Doctor urges the Consuls not to act hastily; he's convinced that the Keeper was attacked by an energy beam from somewhere nearby. He notices that Tremas is carrying a device capable of analysing such energy sources, and Tremas compares notes with him and comes to the conclusion that the Doctor is talking a great deal of sense. Since his guilt has not yet been proven, and since Kassia seems determined to have the Doctor executed, Tremas takes the unusual step of claiming Consular Privelege and placing the Doctor and Adric under his personal protection. Should they break the laws of Traken now, Tremas too will suffer the penalty. Kassia storms out of the sanctum, and finds the bodies of two Fosters who were unlucky enough to encounter Melkur as it returned to the Grove; she hides the bodies, unwilling to let them be found yet.

The Doctor and Adric accompany Tremas to his home, where the Doctor and Tremas compare notes and decide to return to the Grove to search for the missing TARDIS. Adric remains in Tremas' home with Nyssa, who shows him some of her father's scientific equipment; Adric is favourably impressed, and uses it to run an analysis of the energy readings which Tremas had taken before the Doctor and Adric arrived. He finds something quite disturbing, and urges Nyssa to take him to the Grove; the Doctor must be told of this immediately.

Kassia reports to Melkur that she has failed to kill the Doctor and Adric, but Melkur doesn't seem concerned and instead gives her new instructions. Kassia thus returns to the sanctum and summons Katura, Luvic and Seron, to inform them that her husband has been keeping information from them on the nature of his findings. By keeping secrets from his fellow Consuls he has thus cast doubt upon his worthiness as Keeper-Nominate, and must undergo Rapport with the Keeper to prove himself. Seron, however, admits that Tremas kept his research secret at Seron's urging, and volunteers to undergo Rapport in Tremas' place. Kassia is unable to come up with any reason why he should not, and thus seems to have failed Melkur yet again. But again, Melkur doesn't seem displeased -- in fact, when she speaks to him next, he gives her a necklet as a token of her obedience to him...

The Grove is surrounded by citizens who have heard rumours that Melkur has been redeemed and will put an end to the disturbances presaging the death of the Keeper. Proctor Neman, head of the Fosters, advises Tremas that if he enters the Grove now it would seem to validate the rumours, so Tremas takes the Doctor back to the sanctum, to a secret tunnel into the Grove. There, they catch sight of Kassia departing the Grove with her new necklet, but the Doctor stops Tremas from following her. They enter the secret tunnels, pass by the catacomb containing the Source itself, and enter the Grove; there, the Doctor scans the area and determines that the TARDIS has been displaced from the current time-cone. All he needs to do is set up a standing wave for the auto-systems to home in on.

Nyssa takes Adric to the Grove, where she bribes Neman to disperse the citizens. Once the way is clear, Adric picks the lock to the Grove and slips inside, but just as Nyssa is about to follow, Luvic and Katura find her and send her back home. She has no choice but to obey. Adric enters the Grove on his own and gives his analysis of the energy readings to the Doctor; whatever has invaded Traken, it has an energy pattern similar to that of a TARDIS. The Doctor, Tremas and Adric return to the catacombs, where the Doctor uses spare parts around the Source to build a device that will summon back his own TARDIS. But as he does so the Source begins to glow, indicating that the Keeper is being summoned.

The Doctor, Adric and Tremas are locked up in the all-but-forgotten penal quarters of the Consulate, and Kassia bribes Neman to extract a quick confession from them once they awaken. She then returns to the Grove to thank Melkur for fulfilling his promise; now Tremas is in disgrace and will not become the next Keeper. But her service to Melkur is not yet complete. Someone must take Tremas' place as Keeper-Nominate, and Melkur intends that Kassia should be that someone. Trapped, she begs him to release her, but as she does so hears a noise behind her; Nyssa, arriving to fulfil her duties in the Grove, has overheard her pleading with the statue. Kassia orders her to return home, desperately assuring her that all will come to good in the end. Kassia then meets with the remaining two Consuls. Katura and Luvic have no hesitation in naming her the new Keeper-Nominate. And she has no choice but to accept.

Nyssa, meanwhile, fetches an ion bonder from her father's stores and boosts its power. She then goes to the penal wing, where she tries to bribe Neman to let her speak with her father; when Neman refuses, she uses the boosted ion bonder to stun him. The Doctor, Adric, and Tremas have by now worked out that Melkur intends to seize control of the Source by instating Kassia as the new Keeper; they must stop him by any means necessary. Nyssa frees them, but their escape is discovered, and they wait for Tremas' quarters to be searched and then hide there. Kassia is forced to report failure to Melkur, who punishes her by flooding her body with energy from the necklet. But he still needs her alive, and she has no choice but to obey him.

The Doctor demands to be given the plans for the Source Manipulator, and Tremas makes the difficult decision to betray the letter of his Consular oath in order to protect his people. He gives the Doctor the blueprints of the Source, and the Doctor and Adric compare notes and work out how to sabotage the Source Manipulator -- destroying it if necessary to prevent Melkur from controlling its power. The Doctor takes the others back to the Grove, but Kassia was expecting this and has left the way clear for them. As soon as they are within sight of the TARDIS the Fosters emerge from hiding and surround them, but as Neman begins to give the order to shoot them down, a gale-force wind suddenly rips through the Grove. The Fosters scatter in terror as the forces of nature revert to a state of elemental chaos. The Keeper is finally dying.

Kassia goes to the Sanctum, where she urges the dying Keeper to release the Source and go to his rest. As Luvic and Katura struggle to remain upright, the sacred flame above the Keeper's dais flickers and dies, and the Keeper's chair materializes, empty. The natural disturbances settle into a temporary lull, and the Doctor, Adric, Tremas and Nyssa flee the Grove as Melkur gloats over his imminent victory. But even the Doctor doesn't realize the true identity of the twisted, corpse-like creature who lives inside the statue of Melkur. Melkur vanishes from the Grove with the sound of a dematerialising TARDIS...

Melkur seems strangely non-confrontational even as he reminds Katura and Luvic that the Doctor had been rejected by the former Keeper and sentenced to death. Melkur now claims that the former Keeper set these events in motion and that Kassia willingly gave her life to help Melkur ascend to the Keepership. He orders Neman to place the Consuls under temporary house arrest while he waits for the initial period of transition to end; at the moment his powers are still weak, and he vanishes, ordering Neman to place the Doctor under house arrest as well. The Doctor warns Neman that Melkur will use and dispose of him as well, but Neman ignores his warnings and orders the Fosters to lock them all up in their homes. The Doctor is beginning to believe he's met Melkur somewhere before...

Adric and Nyssa return to the TARDIS, where Adric tests the engines -- and finds that something is blocking their dematerialization, preventing them from escaping if necessary. Traken now has only one hope; Adric must follow through on the plans he and the Doctor were discussing earlier, and destroy the Source in order to destroy Melkur. Nyssa is shocked, but accepts that this must be done and agrees to help.

The Doctor and Tremas, locked up together in Tremas' quarters, study the plans of the Source Manipulator and discuss the Ultimate Sanction, a means of disposing of a corrupt Keeper. The Sanction requires all five consular rings, but as the root of the rings' gamma encryption is based on a single prime number, the Doctor knows he can calculate it if given a single ring. Neman then arrives, having been given a consular ring and a necklet by his new master, and Melkur arrives to supervise as Neman orders Tremas to hand over the plans of the Source Manipulator. Some sleight-of-hand between the Doctor and Tremas serves to convince Melkur and Neman that the Doctor hasn't seen the plans yet, and Melkur blasts them into ash. Convinced his safety is secure, Melkur vanishes yet again -- and the Doctor then tricks Neman and his Fosters, bashing their heads together and knocking them out. By the time Neman recovers, the Doctor and Tremas have already taken his ring, bluffed their way into the sanctum and locked the doors.

The Doctor is able to calculate the prime number necessary to implement the Ultimate Sanction, but as Tremas begins to key it in, Melkur appears on the Keeper's dais, his period of transition complete. Tremas and the Doctor are blasted back from the console with three numbers left to key in, and Melkur seizes control of their muscles; the entire Traken Union is now keyed to his biorhythms through the Source. He demonstrates his power by forcing the Doctor to his knees, drawing Neman into the sanctum and forcing Tremas to shoot Neman and then hold a gun to his own head.

Melkur can now force his subjects to build weapons and fleets with which to conquer the galaxy -- but first he intends to drain all knowledge from the Doctor's mind, and become the master of Time as well...

Adric and Nyssa complete their work on a short-out circuit which they connect to the Source Manipulator; they then enter the sanctum to watch the effects of their work, just as Melkur forces the Doctor to step into the Keeper's chamber. Both Melkur and the Doctor vanish -- and when the Source consumes itself and destroys Melkur, the Doctor will be killed as well. The Doctor, meanwhile, finds himself inside a TARDIS control room and finally comes face-to-face with the real power behind Melkur... the Master, who is at the very end of his final regeneration. The Master prepares to use the powers of the Keepership to merge with the Doctor's body, granting himself a new lease on life -- but then, thanks to Adric and Nyssa's sabotage, the Source begins to feed back into the Master's control room. The Doctor flees as the control room begins to explode, and the Master struggles to reach a grandfather clock on the other side of the burning room...

Katura and Luvic stumble into the sanctum as nature reverts to chaos once again. The Doctor reappears in the Keeper's chamber and calls out the last three digits of the Sanction code to Adric, who is only able to input two digits before the rising winds fling him away from the control panel. The Doctor pushes his way out of the chamber, struggles towards the panel and keys in the final digit, banishing Melkur and putting paid to Adric and Nyssa's sabotage as well. The Source, deprived of a Keeper, begins to die, but with seconds to go Luvic leaps into the chair and Katura keys in the acceptance codes, thus putting Luvic on the seat of the Keepership. The Doctor bids Tremas an abrupt goodbye and returns to the TARDIS with Adric, musing that it's time he gave the TARDIS a complete overhaul.