Shayla, one of her world’s most noted physicians, is woken by a loud knocking at her door; a man called the Doctor has brought his desperately ill friend Nyssa for treatment. Nyssa has recently shown evidence of psychic sensitivity, which has left her weak and disoriented; the last time this happened to her, the Doctor induced D-sleep for 48 hours, but it seems that her subsequent recovery was only temporary. Shayla and her apprentice Sabian stabilise Nyssa’s condition, but are unsure what has caused it -- and Shayla fears that the Doctor has exposed Nyssa to great evil. The Doctor avoids her questions until he’s sure Nyssa is all right, and sits by her side until morning. Nyssa wakes from a dream of a hideous voice calling her name, and though disoriented, she instantly recognises the bird outside her window as a crested avar, and realises where she is. In order to find an authority on Trakenite health, the Doctor has taken Nyssa to her homeworld, Traken, 3000 years before its destruction.

Shayla reports the Doctor’s arrival to Consuls Hyrca and Janneus, who are disturbed to learn that an outsider has arrived in the Union, bearing one of their own in need of medical aid. Janneus becomes even more disturbed when the Source warns of danger but fails to elucidate; it’s as though it is unable to divine the patterns at work, or is reluctant to explain. She and Hyrca are thus forced to rely on their own judgement, and the Doctor faces a hostile reception. He doesn’t make things better by flippantly promising to be on his best behaviour, implying that sometimes he isn’t. He’s also taken aback when Shayla reports that Nyssa’s soul has been corroded by exposure to evil, as though evil is a physical presence like cancer or radiation. The Doctor insists that evil is relative; there are beings in the Universe whom the Doctor would consider evil, who consider themselves to be in the right. Even on Traken, regarded as a beacon of perfection, the death penalty is occasionally enforced and the rulers are elected from within the elite by the elite. The meeting does not end well, as the Consuls are angered by the Doctor’s apparent attempts to spread doubt within their paradise. When the Doctor consults Nyssa, she admits that Traken was a more superstitious place in the primeval time before the Keepers, when the Source governed itself; nevertheless, the Doctor is disturbed to realise that Shayla, who was identified by the TARDIS data banks as the foremost authority on Trakenite health, seems to believe that Nyssa has been corrupted by evil spirits. Whatever is wrong with Nyssa, the Doctor’s sure it isn’t the work of the Devil...

Just beyond the edge of the Union, in a fleet of warships which has waited in place for two and a half millennia, Captain Narthex is summoned to attend his master, the living god Kwundaar; however, he chooses to send the devout young Lieutenant Anona in his place. She does not look Kwundaar in the face, as doing so can drive a person mad; when Kwundaar deals with others he usually keeps his face covered. Kwundaar reads her mind and senses her doubts, but knows that she speaks the truth when she vows to keep her doubts private and serve him without question. He is as satisfied as he can be, knowing that every being in the Universe lies and betrays, and he tells her that soon an agent of his will deliver Paradise into their hands. When Anona returns, Narthex doesn’t have to read her mind to know she’s wondering why Kwundaar hovers here on the edge of the Union when he could be out conquering the galaxy. Narthex believes that Kwundaar is obsessed with the one thing he can’t have -- the pure light of the Source. Even if Kwundaar does have an agent on Traken, Narthex is sure that the Consuls will soon be moving in for the kill...

The Consuls summon Shayla to a secret meeting, and tells Sabian to keep the Doctor occupied -- only to find that the Consuls then argue that the necessity of lying proves the Doctor’s evil influence. She must nevertheless confess that Nyssa has been exposed to great evil; though she remains vague about her motives for leaving the Union, in her travels she has seen abominable creatures devoted to the extermination of all other life, and has witnessed the deaths of her father and another of the Doctor’s travelling companions. Despite this, she and Shayla both believe the Doctor to be a good man, but the Consuls aren’t convinced. Without the Source to guide them they must pass judgement themselves, and they choose to expel the Doctor and Nyssa from the Union before their malevolent influence can spread any further. Shayla protests that Nyssa needs the light of the Source to make a full recovery, but the Consuls are unmoved; if it is necessary, then to preserve the Union, Nyssa must die.

Sabian tells the Doctor all about the Source, a sentient sun engineered by the people of Traken which has banished evil and darkness from the Union from all time. Shayla then returns with the bad news, and even as she speaks, Nyssa suffers a relapse and nearly falls into a coma. Shayla plans to lodge an appeal, but it’s clear that Nyssa will die without proper treatment, and Shayla still doesn’t know what’s wrong with her. She thus suggests taking the only course open to them and contacting Kwundaar; his followers are barbarians who pillage and murder at whim, but it’s said that Kwundaar himself is omniscient, and the Doctor’s desperate enough to grasp any chance to save Nyssa. Shayla knows that the Consuls would rather kill the Doctor than let him contact Kwundaar, and thus, despite Sabian’s protests, she takes the Doctor to the spaceport and bribes a merchant captain from outside the Union to smuggle them both away.

As Nyssa recovers, she speaks with Sabian, who is utterly loyal to Shayla and in awe of her abilities. When she inquires after the Doctor, however, Sabian must lie, and he’s not very good at it. Before she can press him for a proper answer, Hyrca arrives and orders them both to attend an emergency meeting to explain why the Doctor and Shayla have vanished after lodging an appeal against the Consuls. Despite her illness, Nyssa insists upon attending in order to defend the Doctor, but she collapses halfway to the door, sensing Kwundaar’s presence in her mind -- and knowing that the Doctor is in great danger...

Shayla is appalled by Narthex and Anona’s lack of concern for the screaming Doctor, but their position is simple; they serve a living god who gives them whatever they desire, and they’re willing to pledge total loyalty to him in return. The Doctor eventually stops screaming, but over an hour passes before Shayla is allowed to collect him. He’s alive but weak; Kwundaar is a powerful telepath, and he had to push very hard to get through the Doctor’s natural psychic defenses. The Doctor will be allowed time to recover before their negotiations continue, but he is puzzled; if Kwundaar is as powerful as the Doctor suspects, what can the Doctor possibly offer him in return for his help? Perhaps if he knew who or what Kwundaar is, he might have a clue. Narthex leaves Anona in charge of the visitors, and although Shayla doesn’t trust her an inch, the Doctor points out that Anona comes from a different background and sees the world in a different way. Kwundaar’s followers know no other way of life than their own, and if the Doctor had the chance, he’d try to save them rather than condemn them, to show them that there are better ways of living than this.

Despite her illness, Nyssa attends the Consular meeting, determined to defend the Doctor. But the Consuls are offended when she questions the awe with which they regard the Source; whatever its power, she knows full well that the Source is just a machine which could be used for evil as well as good. Hyrca and Janneus, appalled by this heresy, question her closely about her travels with the Doctor, and are dissatisfied with the answers; though she claims that she’s learned much and has helped other people, not even Sabian can understand why she would ever choose to leave the light of the Source. And now it seems that her friends have abandoned her; can it be that the evil afflicting her is contagious, and that Shayla fled to save herself from contamination? Hyrca suggests that they may have to destroy Nyssa before the evil spreads, and Nyssa, enraged to hear this superstitious nonsense from a Consul of Traken, overexerts herself and passes out.

Over dinner, the Doctor and Shayla speak with Anona, who’s 18 years old and has no sympathy for those who have suffered because of her actions; after all, her own parents died of an illness for which both the Doctor and Shayla know a cure. The Doctor claims that he helps people to help themselves, but Anona claims that this is exactly what Kwundaar does, only more directly. The Doctor may talk of a “better” way of life, but Anona has all she wants here. Narthex also claims that he has all he wants; the profits of piracy enable him to send his three daughters to the best schools in the galaxy, though he admits they don’t know what he does for a living. Kwundaar then summons the Doctor back into his presence, and the Doctor finds him staring out at the Traken Union again. The light of the Source would destroy him if he approached it -- yet he once walked on Traken in the cool of the evening... The Doctor refuses to help Kwundaar destroy the Souce, even for Nyssa’s sake, even though the people of Traken live in the same state of isolation and conformity which drove the Doctor from his own home world. But Kwundaar knows that the Doctor has already participated in future events which will lead to Traken’s destruction; all he wants is one thing, which the Doctor has seen once before, in the vault containing the Source interface. Kwundaar will strengthen Nyssa’s mental defenses and ensure that she survives until at least the next dawn -- but he dismisses the Doctor without telling him exactly what it is that he expects the Doctor to deliver to him...

Nyssa recovers from her collapse but remains weak, and the Consuls agree to adjourn until the morning. Sabian then takes Nyssa to a spa where the waters of an underground stream surface after passing by the chamber with the Source interface. Though Nyssa is despairing, believing her death inevitable, she begins to feel much better after immersing herself in waters warmed by the power of the Source, and even invites Sabian to join her. The architecture of the spa reminds Nyssa of a temple, and Sabian admits that it predates the existence of the Source and was left standing due to its beauty. As Nyssa and Sabian emerge from the spa, Nyssa finds that her illness seems to have passed completely; though she doesn’t know it, Kwundaar has kept his word to the Doctor. But when she and Sabian return to Shayla’s house they find the TARDIS gone and Hyrca and Foster Etrayk waiting to place them in quarantine. The fact that Sabian has spent so much time in Nyssa’s company without feeling any ill effects must prove that the evil is more subtle and insidious than the Consuls had feared. Nyssa is appalled by this spurious reasoning, but the Consuls have chosen to take action; the TARDIS has been quarantined until they can find a safe way to dispose of it, and now the same is to be done to Nyssa.

Shayla considers Anona’s accusations and uploads the data from her portable medical pad into the flagship’s computers; now, none of Kwundaar’s followers need die from illnesses with cures known on Traken. If she’s expecting thanks, however, she’s disappointed, for Anona thinks her a fool for helping her enemies without reward. The Doctor returns, still puzzled, but as he and Shayla prepare to go, Kwundaar speaks through Anona, telling the Doctor that Shayla must remain to serve his followers as a slave. The Doctor refuses to allow this, and he and Shayla flee while Anona is still disoriented from being used as a mouthpiece. Narthex co-ordinates the guards’ pursuit and sends Anona after them once she recovers, but the Doctor and Shayla reach the docking bay -- and somehow the Doctor manages to open the door, even though the lock had over 14 trillion possible combinations. The merchant ship has been thoroughly looted but is still in one piece, and when the Doctor activates the ship’s drive the pirates are forced to retreat before the blast incinerates them; however, Shayla is uncertain whether the Doctor would have deactivated the engines if they’d called his bluff. The hatch opens automatically as the drive engages, and the launch blast fills the bay with toxic fumes, preventing anyone from following them. The Doctor and Shayla are on their way back to Traken.

The Doctor and Shayla return to Traken in time to see a beautiful sunset, just beyond the armed Fosters sent to arrest them for consorting with the enemies of Traken. However, while Hyrca and Janneus remain deeply suspicious, neither the Doctor nor Shayla are carrying weapons or contagions, and if there was evil in their hearts then the Source would burn them where they stand. The Doctor requests and receives permission to check in on Nyssa, who seems to have made a full recovery and is even teaching the bemused Sabian how to dance the Charleston. The Doctor explains to Nyssa that in her era, her people have been protected by the Source for so long that their natural psychic defenses have atrophied; however, now that the Doctor knows the cause of her illness, he can teach her Gallifreyan meditation techniques which will strengthen her defenses and leave her less vulnerable. First, however, he must report to the Consuls.

Back on Kwundaar’s flagship, Narthex and Anona practice hand-to-hand combat, preparing for the invasion of Traken. Anona flips Narthex by pretending to be injured; his next “practice” blow breaks her nose, and this time, he doesn’t offer to help her up. Before returning to duty, he sets aside time to speak to his daughter, who’s happy to hear from him and tells him all about her new boyfriend. Though she senses he’s hiding something from her, she doesn’t quite realise how difficult this conversation is for him. Soon he will be going to war...

The Doctor attends the Consuls, and is sadly unsurprised when they take little interest in the fate of the merchant captain and refuse to engage in “idle” speculation about Kwundaar. The Doctor thus tells them about his meetings with Kwundaar, and once they’re satisfied that he’s told them everything, they dismiss him and order Shayla to ensure that he and Nyssa leave as ordered. The Doctor offers Shayla the opportunity to come with him, but she chooses to stay, although she now finds Traken to be more stifling than she’d ever realised before. Nyssa bids farewell to the disappointed Sabian, and she and the Doctor enter the TARDIS and depart. Hyrca is relieved to see them go, but Janneus remains unsettled by the experience; she didn’t want to admit it in front of the Doctor, but his questions about Kwundaar’s mysterious origins raised some very valid points. Hyrca believes that the danger has passed, but soon the Source begins to register unusual activity amongst the ships in Kwundaar’s fleet. The Source would surely destroy them if they ventured any closer to the Union -- and yet it appears that they are preparing to attack...

In fact, the Doctor hasn’t left Traken yet, as he’s desperately curious to know what Kwundaar expected him to fetch, and intends to investigate. The Source interface is too well protected for the Doctor to materialise there directly, so he materialises instead in the spa -- more to the point, near the outlet of the underground stream which runs past the vault. He and Nyssa change into swimming costumes and don artificial gills in order to swim upstream, though the Doctor pauses before entering the waters to admire the temple-like architecture of the spa. One invigorating swim takes them to the Source, or rather to the interface, an avatar of the sentient sun which shines down over the entire Union. The Doctor notes that the vault in which it is housed is the same age as the spa -- which, according to Sabian, predated the Source. What were these structures used for originally? And what did Kwundaar expect the Doctor to bring to him, when the only thing in this vault is the Source interface itself? In this era there is no Keeper; the Source maintains itself, and the Doctor couldn’t sabotage it even if he wanted to. Insatiably curious, the Doctor uses the combination provided by Kwundaar to open the protective shield around the Source and look into it directly, but he still can’t figure out what Kwundaar wanted. Deeply disappointed, the Doctor nevertheless concedes that he’s far outstayed his welcome, and he closes up the protective shield, boosting power before he goes to be absolutely certain that Kwundaar can’t get in. He and Nyssa then leave the vault, planning to return to the TARDIS via the Grove rather than swimming back.

Narthex is growing frustrated with his fellow pirates, who seem to be relying on Kwundaar to win the day rather than preparing for battle. Narthex is prepared to die for his god, but he’d prefer not to. But as he tries to force his soldiers into action, Kwundaar himself arrives on the bridge to announce that the Doctor has done his work. Narthex hesitates before giving the command, still fearing the light of the Source, but he does as his god has commanded -- and orders his people to launch their attack at once.

Shayla and Etrayk reach the Consular chamber, only to find Janneus and Hyrca helpless in the face of this threat; Hyrca in particular is more concerned with his own safety than the defense of Traken. Narthex and Kwundaar transmat directly into the chamber, and when Etryak tries to stand up to them, Kwundaar looks into his eyes, driving him mad with terror. Kwundaar senses that the Doctor is nearby, plotting to oppose him, and orders his men to shoot the Doctor on sight; however, he changes his mind when Narthex reminds him of his desire to watch the Doctor die before him. The terrified Hyrca then leads Kwundaar to the Source avatar, and Kwundaar, bitterly amused by the irony of its location, orders Narthex to secure the vault and fetch a certain device from the flagship. As Narthex leaves, he shows mercy of a sort by ordering his men to leave all civilians unharmed; after all, they’ll fetch more when sold as slaves if alive and in one piece.

The sound of fighting dies down outside; with one quick, well-planned strike, Kwundaar’s people have conquered Traken. But the Doctor still has time to prevent Kwundaar from seizing control of the Source itself. He and his friends split up; Nyssa heads for the spa, while the Doctor and Sabian go to the Grove. On their way, they see Kwundaar’s followers carrying something to the vault, and the Doctor, recognising it as the Source Manipulator, gives Sabian a code which he must input into the Manipulator should they become separated. Before they can slip into the Grove, however, Narthex captures them, shooting and stunning the Doctor. He allows Sabian to live, but only so he doesn’t have to carry the Doctor to the Consular chamber himself.

Anona finds Nyssa in the spa, and, unaware that Narthex has already captured the Doctor, she demands to know where the Doctor is. Nyssa claims that he’s already swimming upstream, thus tricking Anona into entering the waters of the spa -- which are still imbued with energy from the Source. The healing water burns Anona like acid, and Nyssa wrestles her gun away, stuns her, and swims upstream to confront Kwundaar. Anona recovers and returns to report her failure to Narthex, who passes on the warning to Kwundaar -- only to find that, of course, he already knows. When Nyssa arrives, Kwundaar is waiting, and Nyssa finds that she is physically unable to shoot him. He is in her mind, as he is in the mind of every native of Traken... Entranced, Nyssa operates the Source Manipulator as Kwundaar commands, reconfiguring the Source to accept his control. Kwundaar sends Narthex to fetch the Doctor, so he can witness Kwundaar’s triumph in person.

The Doctor is recovering, but the situation is dire. Hyrca hopes to negotiate peace, but now that Kwundaar has the Source, what else can anybody possibly offer him? The Doctor has another question -- if Kwundaar is omnipotent, then why wait for so long to seize the Source of Traken, rather than building one of his own? When Anona claims that Kwundaar has been preparing for this day for 2532 years, the Doctor realises that Kwundaar has been hovering on the edge of the Union since the very day the Source was first created. What was he doing before that?

Narthex arrives to fetch the Doctor, and allows Shayla to accompany him; Anona also joins them, to watch her god triumph over his enemies. In the vault, they find Nyssa recovering, and the Doctor realises that she has been experiencing race memories; the people of Traken must have fought Kwundaar before, and the Source is the weapon they built to defeat him. But he’s wrong; Kwundaar now reveals that the people of Traken once worshipped him as a god. He taught them wisdom and the skills of science, and in return, they used those skills to build the Source and drive him from a paradise of their own creation. The spa was once his temple, the vault his inner sanctum. Now he has returned at last, bitter and twisted, to avenge himself by turning the Source itself against his former followers. As he enters the Source, he orders Narthex and Anona to kill the others. The Doctor tries to convince them that he can still stop Kwundaar by using the Source Manipulator to lock the Source into its current configuration. Anona remains loyal to Kwundaar and prepares to shoot him, but Narthex shoots her first, unwilling to unleash a truly omnipotent Kwundaar upon the Universe as long as his three daughters remain free. But before the Doctor can enter the code, the dying Anona shoots the Source Manipulator...

In the Consular chamber, Janneus finally admits to Hyrca and Sabian the ancient truths, which have been passed down to the most senior Consuls throughout the generations. Sabian is shocked to learn that his paradise was founded on a great betrayal, but his reaction seems to confirm that the Union would fall apart if the truth were made known. In any case, they cannot change the past, and surely the Consuls owe it to their people to make the transition to Kwundaar’s rule as smooth as possible? Sabian, however, realises that the Consuls are rationalising their failure to act -- even now, after all they’ve seen, they are trying to convince themselves that Kwundaar won’t be such a bad ruler after all.

The Source Manipulator’s keyboard has been destroyed, but the connections are still active, and Narthex realises that they can wire in the security keypad from the vault’s entrance. But this will take time, and the Doctor therefore gives Nyssa the code and enters the Source to delay Kwundaar. Inside, he learns that Kwundaar plans to destroy all of his followers; he no longer desires the worship of inferior species who would only betray him in the end, and he has used the Source to summon others of his kind, exiled gods who will remake the Universe in their own image. The Doctor tries to hold him back, but Kwundaar strikes him down and emerges from the Source. Outside, Nyssa also tries to hold Kwundaar back using the psychic potential which he had woken in her, but he removes her new powers with a thought and then reads her mind to find the code which will lock the Source into its current configuration. He enters it himself, thus ensuring his victory, and turns on Narthex, intending to condemn him to an eternity of torment for his treachery. But then the Doctor emerges from the Source, sitting on a very familiar chair. The code he gave Nyssa was a ruse; instead of locking down the Source, it transferred control to whomever was inside the Source at the time -- the Doctor. The Doctor is thus able to hold Kwundaar back while Nyssa uses the Manipulator to remove all trace of corruption from the Source. The Doctor then re-opens the shield, and though he gives Kwundaar plenty of time to escape, Kwundaar refuses to go, and burns in the light of the Source until nothing remains.