Somewhere, a man alone in the dark muses on the nature of beginnings. Did the very first event spawn all the good and evil that followed, or were those later inventions? He concludes that the point about beginnings is that the future hasn’t yet happened, and one never knows what will happen next...

Eldrin, the leader of a small and peaceful village, is looking for his daughter Galayana when something falls out of the sky and crashes in the midst of his community. Eldrin advises caution, but one of the villagers approaches the object for a closer look -- and it opens up, spraying him with an unidentified substance. Within seconds, the curious villager is dying horribly. Elsewhere, the innocent Galayana sing-songs the phrase “scaredy cat...”

The Doctor shows C’rizz the TARDIS gardens, which he designed himself, but C’rizz is unimpressed; his people believe that true beauty comes from context, and these gardens are too artificial for him to appreciate. To him, real beauty would be found on a newly formed planet, one still untouched by pollution and war. Charley realises that he’s describing the Garden of Eden. The Doctor offers to show him the next best thing: Endarra, the uninhabited twin world of the planet Caludaar. According to legend, the Caludaari nearly destroyed themselves through war, and in the aftermath, they vowed never to sully Endarra with their presence. For thousands of years, they’ve kept that pledge -- but as the Doctor hovers above Endarra, the TARDIS detects signs of technology on the planet. If the pledge has been broken, war may erupt on Caludaar once again, and the Doctor thus touches down to investigate. The energy traces lead them to what looks like a large shed, but when the Doctor tries to break in with his sonic screwdriver, the shed’s automatic defences open fire...

The shed is some small distance away from the main research complex, which is occupied by three scientists: Professor Arken and his assistants Bronik and Niah. Bronik is becoming worried about their experiments; he suspects that the native primates are more sophisticated than the researchers thought, and he’s concerned for Niah’s safety when she visits the “restricted area” alone to conduct preliminary tests. Arken dismisses Bronik’s concerns and orders Niah to prepare the test subject, a primate, for the next stage of the experiment; it’s unlikely to survive, but that’s part of the point. As Niah reluctantly fetches the animal, the Doctor and his friends trigger the shed’s defences and alarms sound throughout the research complex. In the confusion, the frightened primate knocks Niah aside and escapes. She reports to Bronik and Arken, who are more concerned about the intruder alert -- and what terrible things might happen if the shed’s defences are breached...

Meanwhile, the isolated man continues to pontificate alone in the darkness. He remembers an earnest young student named Jethrel whose high ideals were quickly corrupted once he actually achieved political office. He ponders on the nature of explanations, and how he works out his own reasons for things by watching people. He also considers the nature of jelna wasps, which will not react too harshly if disturbed once, but will sting their foe to death if disturbed a second time -- thus proving that some things really shouldn’t be disturbed...

The Doctor and his friends are frozen in place, unable to move for fear of reactivating the shed’s motion-sensitive defences; however, the Doctor manages to jam the sensors with his sonic screwdriver, just long enough for him and his friends to flee to safety. As they ponder their next move, they encounter the primate that escaped from the research base, and the Doctor notes the scars on its skull -- but as he tries to calm down the panic-stricken primate, a harsh wind blows up, and he and his companions hear a child’s voice chanting “scaredy cat.” Bronik and Arken then arrive and shoot the escape subject with a tranq dart, and while Niah takes the injured subject back to the lab, Bronik and Arken interrogate the newcomers. The Doctor is more interested in getting answers than giving them, and when he spots a fission detrax unit in the lab, he realises that the scientists have been using the primate as a test subject and bombarding its brain with lambda radiation. But for what purpose?

The Doctor isn’t sure what the little girl really is -- a ghost, a mass hallucination, or a psychic projection from the now dead primate. However, he is sure of two things : Arken is tampering with dangerous forces, and the primate deliberately threw itself into the power grid knowing it would die. Disgusted by Arken’s arrogance, the Doctor storms out to try to learn more about what’s happening on this planet; C’rizz follows him, leaving Charley to keep an eye on the others. Outside, the Doctor and C’rizz hear the little girl giggling, and follow the sound to a clearing -- where they find the little girl lying on a rock, asleep or comatose, and covered with moss. As the Doctor and C’rizz examine her body, they are surrounded by a crowd of primates, and the weather takes a turn for the worse as the primate spontaneously begin to chant: “Scaredy cat...”

While Charley and Niah dispose of the test subject’s body, Niah explains that the scientists of Caludaar have always kept watch on Endarra, even though they’ve never been allowed to set foot there. When they discovered that a potentially sentient life form had evolved on the planet, however, Arken -- a prominent figure in the scientific community -- managed to convince his government to sanction illicit experiments that he claimed could potentially eradicate violence and war forever. The mysterious apparition of the little girl has rattled Niah, however, thanks to her grandmother’s old stories of “Yaranaa,” the souls of the vengeful. Charley is more concerned that the primates might retaliate for the death of the test subject -- and her fears seem borne out as angry primitives advance on the base while the weather takes a turn for the worse. Meanwhile, Arken and Bronik discuss the worrying arrival of the newcomers; Bronik fears that the Doctor could pose a threat to the project, but Arken believes that his evident scientific knowledge could come in useful. They are interrupted when the primitives begin bashing their fists against the wall of the compound: simple culture shock, or something more serious?

In the darkness, the isolated man continues to muse to himself. He doesn’t believe that mere curiosity is a virtue that makes life worth living; indeed, whenever he’s looked into the eyes of the dying, he’s seen only regret that their curiosity led to this. He then reminisces about the girl who fell in love with him; she believed that there was good in everybody, and that even the worst could be redeemed if only they had faith in themselves. He proved her wrong.

Surrounded by a crowd of chanting primitives, the Doctor decides to read the little girl’s mind in the hope of finding the key to these events. When he does so, the primitives fall silent -- and yet the Doctor can’t connect to anything, as the girl appears to have no mind of her own. The Doctor is beginning to suspect that this planet isn’t as pure as the legends suggest, particularly when he realises that the “rock” on which the girl’s body has been placed is in fact a deliberately carved altar. A short distance away, he spots a large stone that can only have reached its current position by rolling uphill; when he and C’rizz move it aside, they find that it was blocking a cave, inside which a humanoid skeleton is clutching an obviously manufactured metal sphere. The mysteries are accumulating, but the Doctor believes that the answers may lie in the theory of morphic resonance; the primitives are keyed to this planet’s morphogenetic field, and it’s passed on certain race memories, such as the child’s rhyme. There’s only one way to find out what really happened in Endarra’s past, however, and the Doctor thus takes C’rizz back to the TARDIS, assuring him that Charley will be able to look after herself for a while until they return.

The man wonders aloud whether Charley is supposed to be his lunch, but decides that he’d prefer a lightly grilled fish. He then introduces himself as Eunis Flood, a political prisoner who opposed Arken’s cruel experiments and was thus arrested on trumped-up charges and shipped off to Endarra as a lab rat; he begs Charley to help him escape before it comes to that. Meanwhile, Bronik returns to the lab and admits that he’s locked Charley in with Flood, and the appalled Niah realises that Bronik is cracking under the strain as the experiment runs out of control. Arken refuses to accept that this is the case, and orders her to continue with the research, this time using Flood as the test subject. Bronik returns to the shed to fetch Flood, and tells the outraged Charley that Flood is about to make an invaluable contribution to medical science.

The Doctor uses the TARDIS to scan for signs of technology in Endarra’s history, and the ship takes him and C’rizz four billion years into the past, to a colony full of people who are dying slowly and horribly. The little girl is there as well, alive and real. The colony’s leader, Eldrin, is relieved when the newcomer introduces himself as a doctor, and explains that his people are from Favria, the fourth planet of this system; they have lived peacefully for generations, but now this colony has been attacked for no apparent reason. When Eldrin shows him the metal sphere that unleashed the contagion, the Doctor recognises it as the one he saw in the cave. Analysis confirms that the sphere contains traces of the biological weapon saravin, which the Doctor knows is due to be outlawed and destroyed in a few centuries’ time after Ventriki militants use it on the planet Crestus V. Presumably, a passing cruiser spotted this colony, and the Ventriki callously decided to use the Favrians as guinea pigs for their weapons testing. Only Galayana has escaped infection, perhaps because she has a natural immunity, but now that the Doctor has identified the toxin, Eldrin believes the rest of his people can be saved. The Doctor remains uncharacteristically quiet.

As Arken and Bronik prepare the fission detrax for use, Charley protests their intention to torture an innocent man -- but Niah informs her that Flood is in fact a convicted serial killer who is himself guilty of torturing at least 19 people to death. Before subjecting Flood to his “research,” however, Arken visits him to explain why he’s doing this; years ago, Arken’s son was murdered and his body dumped on a rubbish tip, and ever since, Arken has devoted his life to finding the cause of evil. Flood doesn’t particularly care. Arken takes him to the lab, where Flood tells the uncertain Charley that she’ll have to decide for herself who is telling her the truth. Charley concludes that it’s wrong for him to be effectively vivisected, whatever crimes he may have committed -- but since her presence is proving disruptive, Arken has Bronik expel her from the laboratory.

C’rizz wants to help the dying colonists, but the Doctor refuses, telling him that they can’t afford to change history; they already know that the colony will die out and that Galayana will end up as a disembodied spirit, four million years in the future. However, in front of Eldrin and Galayana, the Doctor keeps up the charade, even offering the friendly young girl a jelly baby. Eldrin notices C’rizz’s discomfort and privately asks him what the problem is, and C’rizz admits that the Doctor is lying and will not supply the colonists with the antidote; however, he decides to do so himself. After he and the Doctor have departed, the Doctor administers the antidote to himself and to C’rizz, and C’rizz realises from his behaviour that he knows what C’rizz has done. But the Doctor then takes the TARDIS three months into the future, and C’rizz sees for himself that his interference had little effect; he didn’t supply the colonists with enough of the antidote, and they all died out anyway. C’rizz, though sickened, now understands that he can’t change history, and he is forced to return to the TARDIS and depart with the Doctor, although the innocent Galayana is still out there, abandoned alone somewhere in the charnel house that the colony has become.

The Doctor warns the others that Arken has inadvertently linked Flood’s mind to the planet’s morphogenetic field. Flood tries to push his way into the Doctor’s mind, forcing the Doctor and the others to flee; however, Flood isn’t yet strong enough to take them all on at once, and he thus forces C’rizz to remain, intending to use him as a hostage to ensure the Doctor’s good behaviour. The pressure of his new powers is giving him a headache, but when he causes the rain to stop with a single thought, he realises just how powerful he has become. To C’rizz’s disgust, Flood exercises his powers by taking over the mind of a nearby primate -- and laughing while he forces the primate to kill his mate while looking into her eyes.

The natives are gathering near the woods, a storm is building, and even if Arken and Niah could get to the base’s armoury, they’d never get close enough to Flood to take him out. The Doctor takes Arken, Niah and Charley back to the TARDIS, where he explains that Flood’s internal pain is becoming externalised on the planet. Four million years ago, an atrocity was committed on the surface of Endarra, and the morphogenetic field of the newly formed planet absorbed the pain and distress of the slaughtered colonists. Now, Arken’s experiments have inadvertently bridged the gap between the memory of that ancient horror and the horrors inside Flood’s mind, making Flood and Endarra one and the same.

The Doctor sends Charley and Arken to ensure that the base’s shuttle is grounded so that Flood can’t escape. Once there, Arken realises that he could take off right now and destroy the base with the shuttle’s weapons, and he begins to power up the engines, ignoring Charley’s protests that this would kill C’rizz as well. However, Flood hears the engines powering up, and reaches out to take control of Arken’s mind. Arken is thus forced to power the shuttle back down and sit in place while Flood comes for him, but fortunately Flood doesn’t realise that Charley is in the shuttle as well. Arken thus orders Charley to remove the power core and flee before Flood arrives, and she has little choice but to do so, though this means abandoning Arken to his fate.

Meanwhile, the Doctor takes Niah to the altar where Galayana’s body resides. Once again, they are surrounded by the native primates, who seem to have a deep-seated urge to protect this place. The Doctor explains to Niah that Galayana’s body is now in a permanent coma, and is just a shell with no spirit within -- but then the spirit of Galayana appears before them, laughing and calling the Doctor “scaredy cat.” When the real Galayana died, after spending weeks on her own in the dead colony, the planet’s morphogenetic field remembered her and preserved her spirit. Galayana lives on as an elemental force, the avatar of Endarra -- an opposing force brought out as a response to the evil that has been unleashed by Flood.

Flood soon discovers that the shuttle’s power unit core is missing, and destroys Arken’s mind in the process of forcing him to reveal what happened to it. Temporarily stymied, Flood returns to the base to take out his frustrations on C’rizz, who has been unable to escape during his brief absence. The equally frustrated C’rizz taunts Flood, challenging him to take a look inside C’rizz’s mind and see for himself the horrors within; for C’rizz too is a killer. Flood’s anger gets the better of him, and it starts to rain as he forces C’rizz to pick up the water bottle on the counter. Even four million years later, there are still trace amounts of saravin in Endarra’s ecosystem, and Flood has the power to tease it back into existence, turning the water in the bottle into pure saravin. He forces C’rizz to drink it slowly, while explaining that he intends to send a distress call to Caludaar, steal the rescue shuttle when it arrives, and flood the atmosphere of his home planet with saravin.

Charley delivers the shuttle’s power unit core to the Doctor, who sends her and Niah to care for Arken while he and Galayana confront Flood. When they arrive, Flood lashes out at the Doctor, but as he starts to peel away the Doctor’s mind, Galayana strikes back at him with all the power of the planet’s elemental forces. He responds by pulling out Bronik’s gun and vaporising Galayana with a single shot. Scoffing, Flood tosses the gun to C’rizz and orders him to shoot the Doctor, and although C’rizz tries to resist, Flood forces him to squeeze the trigger. The blast hits the Doctor in the shoulder, however, and he survives -- and before Flood can force C’rizz to shoot again, a storm wind whips through the base and Flood hears Galayana’s voice in his head. He only destroyed her physical form; she still survives as an elemental spirit. Flood isn’t strong enough to stand against the spirit of an entire planet, and his mind is stripped away under Galayana’s onslaught, leaving him a babbling shell with the innocent mind of a child.