Two generations after the last sighting of Daleks in this arm of the galaxy, there are still Thal patrols out searching for Dalek sleeper units programmed to wake and wreak havoc if ever the Thals let down their guard. One such patrol -- consisting of a captain, five experienced troopers and five young trainees -- is currently searching for signs of Dalek activity in a bug-infested jungle on a planet in the four-world Quadrille system. However, the only Daleks they find in the jungle are long since dead; presumably the Thals’ scanners detected the dead Daleks’ decaying casings.
The Thals return to their shuttlecraft and prepare to depart, but one of the troopers then spots a young Thal child in the undergrowth. The boy flees when the troopers approach him, and when Pelt and Rain follow him, Pelt stumbles across a stagnant pool full of monstrous leeches which leap from the water and attach themselves to every inch of exposed skin on his body. The troopers take Pelt back to the shuttle, and as the young trooper Jomi watches them peel the leeches from Pelt’s skin, he is reminded of the terrible death of his childhood pet, a Grimp named Yo. Yo was crushed between two mining machines when it innocently tried to follow Jomi to school; he had to kill it to put it out of its misery, but failed to do so quickly and only prolonged its suffering.
The small boy returns, and the Thals follow him more cautiously this time, leaving Pelt hooked up to the medical systems in the shuttle. The boy leads them to a cave system, and inside, the Thals find a nondescript man sitting calmly in a chair, reading a book. The man seems friendly enough, but when he learns that the boy led them here, he unexpectedly smashes the boy’s head against the cave wall -- and the “boy” disintegrates into a cloud of insects. These insects have evolved the ability to cluster into a form which their prey has the instinct to protect. Once the Thals had been lulled into a false sense of security and had fallen asleep, the insects would have burrowed into the Thals’ skin and laid eggs inside their bodies, and the larvae would have eaten them from the inside out.
The stranger is clearly either very eccentric or mad; he speaks in rhymes without being able to stop himself, and he does not recall who he is or how he came to be here. Captain Vay decides to resume the mission, but while he’s only expecting trace signals, Rain’s detectors pick up powerful signals from all around them. However, the stranger does not appear to recognise the word “Dalek” or understand why the Thals react so violently to it. The Thals prepare to search the cave for signs of Dalek activity, but as they do so, they encounter another cluster hive in the form of Pelt -- who speaks to them, claiming that the real Pelt has died of his injuries. The horrified Jomi punches him into the wall, scattering the cluster.
The stranger, who decides to go by the title “Professor” until he remembers who he is, shows the Thals around his cave -- and, to his surprise, finds that one of his kitchen walls has vanished, revealing a rainforest and a ruined structure built into the side of a cliff. Vay takes six of his troopers in to investigate, leaving Jomi, Kye and Tar’ant to guard the Professor -- but a translucent barrier then seals off the kitchen once more. Something emerges from the undergrowth and attacks Vay and his troopers, firing bolts of light which disintegrate the trooper Golstar. Another trooper, Amattan, tries to flee back into the kitchen, but gets stuck in the barrier as it solidifies around him, slowly squeezing the life out of him. Tar’ant shoots and kills Amattan to put him out of his misery when Jomi finds that he can’t bring himself to do it.
The Thals decide to leave the cave and circle around to the other side for their friends, only to find that the cave entrance has also been sealed off. Another cluster hive appears, in the form of Kye’s sister Zoe, who was killed as a child after stepping on a buried Dalek mine. The hive leads them to a storage room, where another wall has disappeared to reveal a long tunnel. The Professor seems agitated, sensing somehow that terrible things lie at the end of the tunnel, but he reluctantly accompanies the Thals in. As they proceed along, however, the floor gives way beneath Jomi and Tar’ant’s feet, dropping them into the rainforest. Jomi’s fall is cushioned by soft plants, but Tar’ant falls onto sharp thorns which pierce his body -- and drink his blood.
Jomi attempts to make his way to the ruin on the side of the cliff, but encounters a dormant Dalek in the jungle. Only his quick reflexes save his life when the Dalek revives and attempts to kill him. The Professor then falls out of another of the tunnels which criss-cross the rainforest, but his fall is also cushioned; however, the ground gives way beneath him, nearly dropping him into an abyss, and he and Jomi realise that the ground here is artificial. Buried under a nearby clump of plants, they find abandoned electronic equipment, including a set of surveillance monitors. This is all part of an underground city, abandoned for so long that it has been overgrown by jungle.
The monitors reveal the fate of Jomi’s friends; all of them, including Kye, have been captured and placed in cells in which various torturous endurance tests are being conducted. The Professor peels away one of the flimsy, portable monitor screens, and he and Jomi head for the fortress -- guided by a cluster hive, which takes the form of an old man whom the Professor finds familiar. At the fortress, Jomi is reunited with Dissari; unfortunately, Dissari doesn’t last much longer, as there are active Daleks hidden just outside the fortress. Jomi destroys the Dalek that killed Dissari, and others which are pointed out by the cluster hive. However, there are fewer Daleks than the Professor had expected, and he’s starting to believe it was no coincidence that he and Jomi were dropped out of the tunnel so close to the monitor screens. This is most likely a trap.
The cluster hive leads the Professor and Jomi to a set of doors, and dissipates after telling the Professor that he has seen the old man in a mirror. Jomi opens the doors to reveal a series of monstrous plant and animal Dalek hybrids, some of whom beg him to kill them. The doors seal shut again before he can do so, and the Professor theorises that this apparently abandoned facility was in fact placed under quarantine by the Daleks. His theories are cut short when Jomi opens another cell to reveal a humanoid skeleton wrapped in the skeletal coils of a dead snake and clutching a key which the Professor recognises instantly. Suddenly the Professor remembers everything; his name is “the Doctor,” and he’s here so the Daleks can deliver the coup de grace, the killing stroke granted to a prisoner after torture.
Jomi finds most of his surviving comrades, but is too late to save Fellebe, who falls into the widening abyss in the floor of her cell before Jomi can get to her. The Doctor explains to the survivors that this entire planet is a laboratory in which the Daleks were searching for a way to transplant their fierce willpower and drive into other species’ bodies, transforming them into Daleks in mind, and thus enabling the Dalek species to survive in entirely alien environments. Unfortunately, their drives to perpetuate their species and to destroy or subjugate all others are equally powerful -- and they realised that if they created another, more successful Dalek mutant strain, their creations would turn against them and exterminate the current race of Daleks.
The cluster hive in the form of the old man, the Doctor’s first incarnation, then reappears and reveals the last secret: this laboratory is still active. One of the walls disappears to reveal that the Thals are being observed by hundreds of Daleks. The Doctor informs Jomi that everything on this planet, including the cluster hives, has become imbued with the Dalek factor -- and Jomi, understanding what the Doctor is telling him, shoots and kills Vay, Pup and Rain to save them from their future misery. He has only one shot left after that, but is unsure how to use it.
The Daleks move aside to reveal their Emperor, who apparently regards the Doctor as a force for evil. The Daleks are just trying to populate the Universe with their own kind, ensuring universal peace and harmony, while the Doctor spreads chaos and interferes in their plans wherever he goes. The Doctor now knows that Jomi and his friends were in fact captured years ago and genetically re-engineered in the Dalek laboratories. The Daleks fed them false memories and released them back into the jungle today in order to test their creations, and by surviving, Jomi and Kye have proven themselves to be successful experiments. They must therefore be destroyed for fear that their kind will destroy the current generation of Daleks. Before the Daleks can open fire, however, Jomi uses his last shot to blow a hole in the floor, and he and Kye escape back to the shuttle, believing that their Thal instincts are now working in harmony with the Dalek instincts embedded within them, and that they can shape their own future.
However, the Doctor fears that even this escape has been planned. Jomi and Kye are not the only Thals to have been imbued with the Dalek factor and released back to Thal space. They will pass the Dalek factor on to their descendants, and in the far distant future, when their legacy has been spread throughout the entire Thal race, the Daleks will trigger the sleeping Dalek instincts and turn the Thals into a new race of Daleks. The Doctor was captured long ago and brought here, his memories erased, perhaps to serve as a catalyst in the endurance tests or perhaps simply to be tortured by watching the Daleks succeed over and over again. He vows to fight the Daleks and hold onto his identity, but once again they take his memories from him and return him to the cave to wait for the next “Thal” platoon to arrive...