Millions of years ago at the end of the world, as the Silurian clans prepare for their long hibernation, the scientist S’Rel Tulok is brought before the Justice Chamber, charged with the creation of genetically modified monsters which pervert the course of nature. The penalty for his crime should be death, but in recognition of his past achievements, the judges sentence him to exile on the Earth’s surface. Tulok well knows that this is itself tantamount to a death sentence, and as his friend Sh’vak reluctantly escorts him to the airlock, he pleads with her to see reason and help him save his creatures from those who would destroy them. But it’s too late; the Silurians have passed judgement, and Tulok’s creatures will also be released onto the surface, to face the justice of the natural world...

The TARDIS materialises in a jungle somewhere; the Doctor hasn’t told Evelyn where they are, but he’s reading The Encatadas by Herman Melville, which would give her a clue if she’d ever read it herself. She’s never liked Melville, however, finding him pompous and overblown -- so she isn’t surprised to learn he’s the Doctor’s favourite author. As she and the Doctor make their way through the scrub, she notices that the birds aren’t terribly frightened of them. There appears to be a clear path through the undergrowth, and Evelyn soon finds out why; this is the path the giant tortoises take to fresh water. They’re on the Galapagos Islands, which were named after the Spanish word for “tortoise”. As the Doctor and Evelyn follow the tortoise to water, they encounter a young man shooting at the birds, collecting samples for later study. The Doctor has already prepared for this encounter, by passing word of his arrival to this man via his colleague, Doctor John Stevens Henslow of Cambridge. Posing under the name of Doctor Albert Einstein, the Doctor claims that he and Evelyn are students of geologist Charles Lyell, and that they are here to survey the islands. When their new friend learns that they’ve left their “boat” on the other side of the island, he offers to ask Captain Fitzroy if they can stay on the Beagle for the night, and Evelyn finally puts the pieces together. The Doctor has brought her to meet one of her heroes, Charles Darwin, in the days during which he will first form his theories of evolution and natural selection.

Elsewhere, in the colony of Baquerizo Moreno, a trial is underway. Fisherman Emilio Rodrigues stands accused of conspiracy and treason, and he cannot defend himself -- he’s raving mad, too terrified by what he has seen to speak coherently. Despite the pleas of Emilio’s sister Greta, Governor Lawson sentences him to death by hanging, and the guards strike the wailing Greta to one side as they drag Emilio off to the jail. Lawson dismisses the jail guards, claiming that there’s no way Emilio can escape from a locked cell -- and then contacts his masters to inform them that he’s sent them a new specimen, the one who disturbed them at the lake. The sight of the creatures has driven Emilio mad, and he can feel terrible things happening to his mind as the monsters from the lake return to the jail and take him away...

As Darwin leads the Doctor and Evelyn to the town, a penal colony for political prisoners from Ecuador, he discusses the strange tameness of the native birds and the even stranger fact that they seem to have learned to fear humanity over the past 150 years. The Doctor prevents Evelyn from prompting Darwin any further; he must make his discoveries on his own. They continue on to the town meeting hall, where Darwin introduces them to Governor Lawson and Captain Fitzroy; they are welcomed to the table, but Evelyn is taken aback to find that everything on the menu is based on tortoise. It’s the staple diet of the islands, and Lawson has eaten it so often that he can identify each one’s island of origin by its distinctive taste. As Darwin puzzles over this, Lawson recognises one of the serving girls as Greta, and cruelly taunts her about her brother’s execution, driving her from the table in tears. The Doctor, furious, storms out to console her, telling Evelyn to stay with Darwin.

Fitzroy and Lawson discuss the strange fossils recently found at Punta Alta; they seem to take the discovery in stride, but Darwin is far more concerned by the implications of the fossils’ existence. Lyell believes that the fossil record is thousands of years old and that it records numerous mass extinctions; and Cuvier has noted subtle changes in the fossils as they approach the modern era, suggesting that the species altered as time went on. And yet according to the Bible this world was created as it is 6000 years ago and there was but one Flood, so what is Darwin to believe? Dinner comes to an end, and the crew of the Beagle prepare to take their leave; a thick fog is coming in and Lawson, who has other duties to attend to, advises them to be off as soon as they can. The Doctor has not yet returned, but Fitzroy agrees to let Evelyn spend the night aboard the Beagle. As their boat makes its way through the fog, all eyes are peeled for the lamps which will guide them back to the ship; but to Evelyn’s surprise, as the Beagle comes into view, she glimpses another set of lights... under the surface of the water.

Evelyn finds Darwin writing his journal entry for 19 September 1835; he assumes that she’s having trouble sleeping because she’s worried about the Doctor, but she’s confident that he can take care of himself and is just curious about what’s keeping Darwin awake. Darwin admits that he’s having trouble reconciling his discoveries with his beliefs. The finches he’s studied are slightly different on each island, as if the subtle variations in each island’s environment are causing variations in the finches themselves. But if diversity within species is the result of some natural process, where does that leave the hand of God?

The Doctor and Greta awaken inside another prison cell, far below sea level if the air pressure is any indication. Emilio is in the cell with them, but he’s still raving, and the Doctor now knows why. He hypnotises Emilio to give him a chance to rest, and explains to Greta that the creatures they saw, Silurians, are the original inhabitants of the Earth, founders of a highly sophisticated culture which ruled the Earth while humanity was still in its infancy. When the Earth was struck by a terrible catastrophe and nearly destroyed, the Silurians retreated into hibernation chambers to sleep it out, but they never woke again, and in their absence the world renewed itself and brought forth life once again. Now somehow a clan has woken, and the sight of them has shattered Emilio, waking buried instincts and driving him back to the mental level of one of his primitive ancestors. The Doctor tries to help him, unaware that his conversation with Greta has been monitored by Sh’vak, who reports to Tulok that one of their captives seems to know of their species already. Tulok wants to kill the Doctor right away, but Sh’vak wishes to question him further to find out if any other clans survived after all. Tulok reluctantly agrees to let her do so.

Morning has dawned, and Evelyn and Charles are on their way back to the island to inquire after the Doctor. But Charles’ thoughts are still on the islands’ birds, and the way in which they have learned to fear Man. Birds do not learn from the past, nor do they pass knowledge on to their children -- at least not deliberately. But amongst a large population of birds, some must naturally be more timid than others, and as the bolder ones would approach predators and die, only the timid would survive. Somehow they must pass this trait on to their descendents, so that eventually the population consists only of the more timid birds. This process may also explain the variation in the size of the birds’ beaks; in times of food shortage, a bird with a larger beak would be able to eat more food and would thus stand a better chance of survival. Darwin is puzzled when Evelyn refers to this process as the “survival of the fittest” -- after all, that’s what “fittest” means -- but he believes that he’s on to something...

The Doctor explains to Greta that every human being retains instincts passed down from their ancestors, and that seeing the Silurians has triggered memories buried so deeply that Emilio has been overwhelmed by his fear. The Doctor hypnotises Emilio once again, and sends his mind back to his first sight of the Silurians; it was a hot day, and Emilio went into a cave to shelter from the sun only to find monsters in the darkness. The Doctor helps Emilio to push the fear to the back of his mind, but before he can help any further, Sh’vak arrives and takes the Doctor to her laboratory for interrogation. The Doctor notes that she has been augmenting bacterial cultures, but before he can investigate she manacles him to a chair and interrogates him, demanding to know how he knows of her people. He’s disgusted when he realises that she’s only trying to find out how much of a threat the human race poses to her people; as far as she is concerned, humanity is an infestation which must be eliminated from her world. The Doctor tries to convince her that the only real solution is a peaceful solution, but she won’t accept this, nor will Tulok when he arrives. Instead, he orders the Doctor to tell them everything he knows about the weapons and technology possessed by humanity, so the Silurians will be prepared when the time comes to destroy the human race.

Darwin and Evelyn contact Lawson, who informs them that his guards have found no sign of the Doctor as yet. Darwin is puzzled when Evelyn rudely storms out, but when he follows her she points out that Lawson had already left the meeting house by the time they realised the Doctor was missing. So how did he know to send his guards out? Certain that Lawson knows more than he’s saying, Evelyn takes Darwin to the jailhouse to investigate further, unaware that Lawson is monitoring their every move. They also find the jail empty and unguarded, and when they investigate they are nearly caught in the same cell which trapped the Doctor and Greta. The front door of the jail locks automatically at the same time, and a secret passage opens up in the cells. As it’s the only way out and Evelyn doesn’t fancy waiting for someone to capture her, she pulls a portable torch from her handbag, glossing over its existence to the bemused Darwin. Darwin follows her into the passage, shaken by what he’s seeing...

Tulok questions the Doctor about the Beagle, thus proving that he knows the people on the boat are different from those on shore. Since all humans are the same to the Silurians, this implies that someone on the surface has been keeping them updated, and it isn’t difficult for the Doctor to work out that this must be Lawson. Tulok, irritated, tortures the Doctor until he admits that the Beagle only carries primitive projectile weapons and that the human race has not yet discovered the sciences of genetics or nuclear fusion. Tulok leaves Sh’vak to continue the interrogation while he answers a video communication from Lawson, but Shv’ak is unwilling to cause another creature unnecessary pain, even an ape creature; and she wants to know whether any other Silurian clans did survive. The Doctor is quite interested to learn that Tulok told her their clan was the only one to survive, but before he can pursue this any further, Tulok contacts Sh’vak and orders her to lock up the Doctor again while they attack the Beagle. The Doctor, appalled, begs Sh’vak to intervene, but she refuses. Meanwhile, Greta tries to console Emilio, but another Silurian arrives at their cell...

As Evelyn and Darwin descend, they hear the sound of machinery, and see that the passageway is getting wider -- and smoother. The passage opens up into what appears to be a mausoleum full of coffins, but there are pipes and valves everywhere, and the room is full of algae and the smell of seawater. Darwin takes a closer look at one of the coffins, and finds the rotting skeletal remains of a bipedal lizard with a third eye socket. It’s like nothing he’s ever seen before, and he’s beginning to wonder whether the process he’s theorised, of “descent through modification”, could result in more than just variation between species -- perhaps over time, such variants could become entirely new species in their own right...

The Beagle is under attack by a Myrka, and the Doctor knows that the crew’s weapons will be of no use against it. The creature lives in the cold darkness of the ocean floor, and thus the Doctor urges Fitzroy to empty the lamp oil onto the waves and set it alight, hoping that the heat and light will drive the Myrka away. But the creature continues to attack, electrocuting any crewmen unlucky enough to get in its way. The Doctor realises that the Silurians must have planted a homing beacon on board the Beagle; the Myrka will not stop attacking until it has found and destroyed the beacon. The crew search the ship without success, but as the Myrka claws through the hull, Greta runs to the Doctor for protection and his sonic emission detector goes wild. As he’d feared, the Silurians have implanted the beacon inside Greta’s body. Greta may not understand all that’s happened, but she understands that the monster is going to smash the ship apart just to get to her -- and before the Doctor can stop her, she throws herself into the Myrka’s jaws, giving her life to save everyone else. Once the beacon is destroyed, the Myrka retreats as the Doctor watches, sickened.

Sh’vak realises to her dismay that Tulok used a sonic implant to lead the Myrka to its prey, despite the fact that the use of the implants in Myrka hunts has been forbidden for excessive cruelty. But Tulok insists that the ape creatures must be destroyed by any means necessary. Sh’vak has already prepared an airborne bacterial culture to rid the Earth of its infestation, wiping out all humans but the newborn within minutes, and Tulok intends to test it on the two new specimens they’ve captured in the hibernation chamber. Evelyn and Charles are now in the cells, and Darwin is struggling with the terrible implications of what he’s seen -- intelligent lizards with facial features like those of men. The process of “descent through modification” must have caused the lizard species to evolve into the shape most suited for existence on this earth; and who is to say that Mankind is not the result of the same process? To Evelyn and Darwin, the creatures are nothing more than modified lizards; can it be that to them, humans are nothing more than modified apes? The implications are horrifying; Eden is a myth, a lie. Mankind is not set apart from nature; men are animals, and nothing more.

The oil fire has burnt itself out, and as the Beagle’s crew sets about repairing the damage, the Doctor learns that Evelyn and Charles returned to Chatham Island to rescue him; he will have to reciprocate. Fitzroy determines to go with him and get to the bottom of things. They return to the colony and confront Lawson, as the Doctor knows that the Silurians must have used their influence to bend the weak man to their will. He hypnotises Lawson, who confesses that he has delivered many people who would not be missed to the Silurians, including Charles and Evelyn. The Doctor finds and destroys the video link which enables Lawson to communicate with his masters, and destroys the remote controls for the prison after jamming open the passage to the Silurian bunker. He then offers to help Lawson break free from the Silurians’ influence, but to Fitzroy’s disgust, Lawson refuses; he can’t bear to live free with the consequences of what he has done. As the Doctor and Fitzroy depart, Lawson begs his masters to forgive him, but he cannot be heard. However, before the Doctor smashed the video link, Tulok and Sh’vak heard Lawson betray them. Tulok therefore orders Lokan not to test the bacterial culture on their two prisoners after all; he has another subject in mind.

Evelyn is becoming worried by Darwin’s mood swings; one moment he’s rattilng at the bars of his cage, seeking a way out, and the next he sinks into gloom as the implications of his discovery weigh on his mind. He once studied to become a surgeon, but failed to apply himself for fear of what he was seeing -- men with the same bloody organs as those he’d seen in the bodies of animals. Even then he feared that despite all of his beliefs, men were not made in the image of God. Everything he has seen so far fits his theories of natural selection, but if this is the case, then the lizard creatures, with their third eyes and their power to render Charles and Evelyn unconscious without physical force, must be the more advanced species. And Charles knows only too well what any species does to its inferiors.

The Doctor and Fitzroy make their way to the hibernation chamber, where Fitzroy stares about in shock as the Doctor describes the disaster which drove the Silurians to this extreme. He has never quite understood why they remained in hibernation... until now, when he finds the control unit for the hibernation chamber, and realises that their failure to awaken was no accident. He and Fitzroy are forced to hide in a side tunnel as a party of Silurians passes through on their way up to the settlement, and as they proceed they find the tunnel growing colder and icier... until they find themselves in a chamber of horrors where the corpses of the missing prisoners are hung on hooks like slaughtered cattle in a larder. Which, Fitzroy realises, is just what they are. The Doctor may claim that it’s part of the natural order for species to prey on their lessers, but Fitzroy will not accept this; human beings are not cattle, bereft of culture, morality or immortal souls. To the Silurians, however, this is indeed all they are -- and when Sh’vak catches them in the larder, she strikes down Fitzroy with her third eye and refuses to listen to the Doctor’s attempts to tell her something quite important.

Lawson is lost without his masters, and is pathetically grateful when Tulok and his people arrive. But Tulok rewards him for his loyalty by handing over a container full of the bacterial culture which will destroy humanity, and ordering him to open it. Lawson does so, believing this to be a test of his loyalty... and the bacteria strips the flesh from his bones within minutes. The test is satisfactory.

Sh’vak throws the Doctor and Fitzroy into the cells with Evelyn and Darwin, still refusing to listen to the Doctor’s attempts to speak with her. Instead, she returns to her lab to wait for Tulok’s return, and while there she listens to the conversation in the cells. She learns little more of interest; the Doctor knows of the disaster which drove the Silurians into hibernation, and Darwin is struggling towards an understanding of natural selection, but they are still far from the truth. Sh’vak can still remember opening the airlock at the last moment and allowing Tulok to survive, refusing to condemn the man who had once saved her life. Even then, Tulok’s only thought was for his creations, but he was too late to save them, for the Triad had already expelled them onto the Earth’s poisonous surface. They didn’t object when he used his techniques to improve the beasts’ flavour and their ability to resist disease, but when he used genetic modification to give them intelligence and the ability to cultivate themselves without the Silurians’ help, this was going a step too far. All of his work was destroyed, and the furious Tulok vowed to have his revenge...

Darwin and Fitzroy are horrified by Tulok’s claims, but they cannot resist when Tulok uses his third eye to hypnotise them, forcing them out of the cell to help load the bacterial cultures onto the submersible. Evelyn and the Doctor are left locked up to ponder Tulok’s revelation that humanity is in effect a genetically modified flock run wild. It seems there’s nothing they can do while locked up here, but the Doctor suspects that Sh’vak is listening in, and he therefore tells Evelyn that he examined the timing mechanism in the hibernation chambers... and found that it was deliberately disconnected. Someone didn’t want the Silurians to wake up. Appalled, Sh’vak checks for herself, and discovers that this is true. She confronts the Doctor and Evelyn, but is forced to admit that Tulok must be responsible. When the Triad destroyed his work, he destroyed them; his revenge was to deprive the whole Silurian race of its future. By showing compassion to Tulok, Sh’vak is responsible for the destruction of her people.

Sh’vak now understands that the Silurians brought this fate upon themselves in their arrogance; the Earth does belong to humanity now, and Sh’vak must stop Tulok from releasing the bacteria. To the Doctor’s frustration, however, she departs to deal with Tulok herself, leaving him and Evelyn locked in the cell. Darwin and Fitzroy then return, having completed their work; the Doctor snaps them out of their catalepsy, but Darwin remains stunned by Tulok’s claim to have created Man. The Doctor, realising that Darwin is on the verge of abandoning his belief in natural selection, assures him that the theory still holds; there may be no fossil record of the Silurians, but that’s only because they were intelligent enough to avoid the tar pits and amber traps which preserved the bones of lesser species. The same will happen to Mankind one day; they will pass on from this life, leaving no tangible legacy, all of their culture and greatness a brief candle in the darkness.

The submersible is ready to leave, and Tulok goes in search of Sh’vak, only to find that she has learned the truth. He insists that the cowards who condemned his work deserved to die; now he will create a new world order, in which he will be a god. Sh’vak, finally recognising his evil, tries to strike him down with her third eye, but he proves more powerful and strikes her down instead. As he prepares to leave, however, he overhears the Doctor chastising Fitzroy for claiming that he and Darwin are better than savages; how can they expect the Silurians to treat them as civilised beings then they regard their fellow men as inferior? But Darwin realises that Fitzroy has a point; if the men of today are more advanced than the primitive apes which the Silurians farmed, perhaps they are not as susceptible to the Silurians’ mental control, and perhaps that’s why the Silurians fear them. Tulok, enraged by the thought that he should fear his own creations, has Lokan send a guard to the cells to kill the captives immediately.

As the Doctor tries to figure out how to escape, Tulok contacts his captives, informing them that Sh’vak is dead and that a Silurian is coming to kill them. But as he signs off, Sh’vak arrives; she survived his attack and has dealt with the Silurian sent to kill them. The Doctor takes everyone back to the control room, where he contacts Tulok and claims that he and his friends are capable of resisting Tulok’s control; furthermore, he has set the bunker’s fusion reactors to overload and they will explode within fifteen minutes. Lokan detects a power surge in the reactors, and the furious Tulok sets off to show the Doctor just who is the inferior species. In the control room, Sh’vak hides and prepares while the Doctor tells Darwin and Fitzroy to concentrate on something they believe in absolutely, anything which will help them to resist Tulok’s attempts to control their minds. He then gives Evelyn a certain device which he’s picked up, telling her to slip aboard the submersible while they keep Tulok occupied, and plant the device on board.

Tulok arrives and orders the Doctor to step away from the reactor controls; he refuses, and points out that if Tulok uses his third eye as an energy resonator, he risks blowing up the control panel and precipitating a meltdown. Infuriated, Tulok turns on Charles and Fitzroy, and orders them to kill the Doctor. They struggle to resist, but Charles’ faith in God is no longer strong enough... and he thus turns to his belief in the process of natural selection. Whatever Tulok may have done to Mankind’s ancestors, he is no God, and the species has changed in his absence. Despite all of Tulok’s efforts, he fails to turn Charles and Fiztroy, and with only two minutes left before the reactors explode, he flees, leaving the humans to die. The Doctor admits that Sh’vak used her own mind to create a mental barrier, helping Fitzroy and Darwin to resist Tulok... but the strain has proven too much for her, and she dies, asking the Doctor to tell the other surviving clans what has happened here.

Lokan nearly catches Evelyn planting the device in the submersible, but she thinks quickly and claims that Tulok sent her to tell him that the other apes have been destroyed. Lokan accepts her claim and returns to the bridge, and Evelyn escapes. Soon afterwards, Tulok arrives, but he refuses to discuss what happened or why the reactors are still overloading. Lokan, puzzled, launches the submersible and prepares the bacterial warheads for launch. But before he can do so, Evelyn gets back to the control chamber and reports success, and the Doctor activates the homing beacon controls and flees with his friends as the reactors go critical. Lokan detects a large mass approaching, and by the time Tulok realises that the Doctor has somehow planted a sonic emitter on board, it’s too late; the Myrka attacks the submersible, and destroys it.