The TARDIS encounters turbulence in the Vortex, as if it’s been caught up in the wake of another ship -- or as if another ship is trying to ram into it. The Doctor manages to materialise safely on a desolate, windswept planet, and after an initial look around at his inhospitable surroundings, he decides to depart. Before he can do so, however, he is shot and falls to the ground. Disoriented, he awakens to find a familiar face tending to him: his former companion, Peri, who’s a couple of decades older than she was when he last saw her. He’s horrified to learn that she still thinks he abandoned her on Thoros Beta, and explains that he was kidnapped and placed on trial by the Time Lords; by the time he’d sorted that mess out, he had been told that she was happily married to King Yrcanos. It seems that their marriage wasn’t as happy as he’d believed, however, and the remorseful Doctor apologises for failing to check up on her.

The Doctor realises that he can’t remember what happened before he landed on this planet, which Peri identifies as Refiloe. She explains that she crashed here eight months ago; the TARDIS presumably responded to her distress call, but when the Doctor emerged, he fell from a cliff ledge and was knocked unconscious. He’s been out for three days, and in that time, the natives have taken the TARDIS into their temple, believing it to be a gift from the goddess Sohile. Peri and the Doctor are being treated as honoured guests, perhaps as spirits from the gods -- but the villagers still aren’t entirely sure what to make of them. The Doctor realises that Peri is also wary of him, but all he can do is apologise for his uncharacteristic behaviour on Thoros Beta and assure her that he’ll never let her down again.

The Doctor and Peri are greeted by the village’s high priest, Damus, who tells them that Sohile’s power has reached out from the “shining cabinet” to grant miraculous healings. Peri reminds Damus that some villagers have lost crops and livestock, and that one of the elders died yesterday, his body aging decades overnight. However, Damus insists that Sohile only punishes those who harbour evil in their hearts -- and he’s watching the Doctor and Peri closely to determine whether they really are messengers of the goddess. Until he is certain, he will not allow them to enter the temple, which means that the Doctor is effectively cut off from the TARDIS with no way to investigate the mysterious visitations, which began shortly after his arrival. Peri suggests seeking help from the village’s chief, Hamiyun, but before she can lead the Doctor to him, the Doctor suddenly feels giddy and collapses. As if in a dream, he hears the voice of Rashaa speaking to him, overcoming his resistance...

The Doctor recovers to find Peri and Hamiyun tending to him, and assumes that he hasn’t fully recovered from his fall. Once he has regained his wits, Hamiyun questions him about the shining cabinet. Damus is young and ambitious, and Hamiyun fears that he’s been too quick to claim that Sohile’s power is at work; for his part, Hamiyun believes that the elder who died was a good man who didn’t deserve his fate. However, he can’t challenge Damus without proof, and even he can’t grant the Doctor permission to enter the temple and investigate. As the Doctor ponders his next move, a nearby grain store collapses, and the Doctor discovers that the building’s timbers have aged, confirming his suspicions that the odd events are being caused by time distortion. He suspects that someone has been conducting illegal time experiments on this primitive planet, and that they’ve used the arrival of the TARDIS as an excuse to begin experimenting on the natives. However, the Doctor needs to access the TARDIS to track down the source of the time distortion, which means he will have to sneak into the temple in disguise.

The Doctor then suffers another seizure; again, he hears Rashaa’s voice in his head, and when he looks about, he sees not a lush and fertile village but a devastated wasteland. Again, Rashaa pushes him back under, and he recovers with no memory of what he’s seen -- just an abiding impression of death and despair, and a sense that someone is watching him. To his shock, Peri informs him that he’s been unconscious all night. With little time to prepare, he and Peri disguise themselves as an old woman and daughter, and slip into the temple with the rest of the congregation. Once inside, it’s all too clear what’s happening; the TARDIS sits before the congregation, its windows cracked, the bright light of raw chronon radiation shining through. The Doctor realises that his ship must have experienced some catastrophic event in the Vortex, powerful enough to damage its outer shell and affect the Doctor’s memory -- and now the entire village is in danger.

Hamiyun tries to protest this cruel punishment, but as he speaks, another wave of time distortion sweeps out of the temple -- and puts out the fire. Presumably the TARDIS has exerted some modicum of control over the energies being released. Damus has little choice but to free the Doctor and Peri and allow them into the temple, since it seems that Sohile has shown them mercy. Inside the temple, they find that the father of the girl who was aged during the ceremony has returned to seek forgiveness, as his entire family has come down with the same illness. Before the Doctor can stop him, the man steps into the light and is aged to death -- and the Doctor realises that the chronon radiation has also accelerated the growth of the virus within his body, which is why it began spreading more rapidly after his daughter was exposed to the radiation.

The Doctor sends Hamiyun and Damus to isolate the sick family and prevent anyone else from entering the temple, while he takes a blood sample from the dead man. As soon as the coast is clear, he and Peri nip into the TARDIS; fortunately, it’s safe inside, as if they’ve passed through into the eye of a storm. The Doctor finds no trace of the virus when he analyses the blood sample, but he then experiences a momentary giddiness, and when it clears, the images he sees on the TARDIS medical scanner confirm that the virus has evolved into a more potent and deadly strain. The Doctor sends Peri to fetch antibiotics while he prepares a vaccine, but when they leave the temple, they find a mob of frightened villagers trying to get inside, still convinced that the power of Sohile will save them. Hamiyun’s guards are struggling to hold them back, but in the confusion, few of the antibiotics are distributed -- and if the villagers are exposed to the chronon radiation again, the virus will evolve even further, rendering the vaccine useless.

The Doctor collapses again while pondering his next move. Rashaa is allowing him to get close to victory in order to pluck it from his grasp at the last moment, thus making his despair all the stronger; however, he’s able to resist her control long enough to glimpse her time capsule nearby and realise that he’s not feeling very well himself. Rashaa pushes him back under, and he finds himself back in the village with little memory of what he saw during his faint. To his horror, Peri reveals that he’s been unconscious for two days -- and that the villagers stormed the temple and exposed the virus to further waves of chronon radiation. The Doctor’s vaccine is now useless, and Peri has come down with the illness herself. The Doctor realises that he now has no choice but to deal with the problem at its source -- by jettisoning the TARDIS interior, leaving himself and Peri stranded on Refiloe.

As the Doctor and Peri approach the temple, they encounter Hamiyun, who intends to burn the shining cabinet. He attacks the Doctor, blaming him for the disaster that has befallen his village, but Peri insists that the Doctor is the only one who can put things right now. Hamiyun reluctantly accompanies them to the temple, which is now littered with bodies, including that of Damus. Peri collapses, her body going into shock, and while Hamiyun tends to her, the Doctor enters the TARDIS, collects all of the portable medical equipment, and prepares to shut down his ship. Peri recovers and follows him inside, and though she offers to help the Doctor, he refuses, insisting that he be the one to finish it. The TARDIS resists him as he pulls the final lever, but he pulls it home nevertheless, believing that he has no choice. Peri then collapses, and the Doctor drags her outside with the medical equipment as the TARDIS’ interior begins to collapse in on itself.

Outside the Doctor’s nightmare, Rashaa and the Agent watch, amused. Rashaa has planted the seeds of the dream, and the Doctor’s mind has filled in the rest of the story himself. His mind occasionally resists the implant’s influence, but Rashaa has always been able to push him back under, and the implant has suppressed his memory of the real world. And since the nightmare has been pushing him forward with no time to think, he’s responded to what he thinks is a real threat -- and destroyed his only means of escape. Within three cycles, the toxic atmosphere of this planet will kill the Doctor, and the Agent’s future will be secure.

The Doctor takes a blood sample from Peri and injects it into himself, hoping that his body will be strong enough to fight the virus and generate antibodies he can use to cure his friend. However, as Peri’s fever increases, the medical scanners reveal that there are no antibodies developing in the Doctor’s body -- and Peri dies before his eyes. Grief-stricken and unable to understand what’s happened, the Doctor sets the scanner for a wider range, and discovers that there’s no trace of the virus in his body at all. However, he is suffering from internal bleeding and serious trauma to his soft tissues, and there’s alien material embedded in his cranium. The Doctor uses his portable surgical unit to remove the alien bioelectric implant from his brain -- and Hamiyun, Peri, the temple and the village vanish from around him, revealing that he’s in the wasteland he saw in his “visions,” and that there’s a time capsule sitting near the undamaged TARDIS.

The Doctor realises that he’s been tricked, and despite the damage caused to his body by the toxic atmosphere outside, he forces his way into the TARDIS and halts the collapse before it spreads any further. Now that the implant has been removed, his memories are clearing, and he realises that he was forced down onto this planet by the time capsule outside. He crosses over to the time capsule, which he determines is a Nekkistani vessel now occupied by a mercenary of another species. Fortunately for him, she’s left the control room for a moment, and he is able to prepare for her return. When Rashaa enters the room, the Doctor fires the implant into her body, using the gun she used on him earlier, and dons the control helmet. Rashaa plucks the implant out of her fur, revealing that it did not penetrate her flesh, and drags the Doctor out of the control unit. He is too weak to put up a struggle as she shackles him to the wall, revealing that she’s been employed to kill him by someone who has learned that the Doctor will otherwise kill him in the future. Though disappointed that the Doctor escaped her carefully set-up trap, she has no objection to killing him more directly -- and she thus tears both hearts out of his body.

Or so she believes. In fact, the implant did penetrate her skin after all, and she’s experiencing an illusion generated by the real Doctor. He now establishes that his hallucinatory self is too badly injured to regenerate, and slips back to the TARDIS as Rashaa crows with victory. He intends to track down Rashaa’s employer, and while he’s at it, to find the real Peri and fulfil his obligations to her at last -- but neither he nor the TARDIS is in any fit state to go searching after the damage they’ve suffered, and the Doctor thus decides to take his ship somewhere they can both relax and recuperate from their injuries.