In the 25th century, during Earth's empire period, Earth decided to colonize the planet Solos, one of the richest fuel sources in the galaxy. Solos was populated by indigenous people who were mostly nomadic farmers or warriors, living in small villages with stick cottages. But the atmosphere of Solos contained a nitrogen isotope which produced a poisonous mist during the daytime when it reacted with sunlight. Because the Earthmen - known as Overlords on Solos - could not survive on the surface for more than a few hours without a mask, they instead constructed a skybase orbiting the planet. The Overlords then began to mine Solos for fuel, but after five centuries of burrowing through the planet, Solos' fuel reserves were practically exhausted. And as a side effect, the pollution caused by Earth's mining operations sparked mutations in the planet's population. The Overlords called these creatures "Mutts", and decided that they must be hunted down and killed. Any mutants which escaped the Overlords fled into the disused mines to hide. In the 30th century, conditions on Solos began to change. An academic named Sondergaard came from Earth to study Solonian culture, but he disappeared. Earth decided that since Solos, now one of its last empire colonies, was no longer a viable fuel source, its only remaining value was as a planet for colonization - and to make it habitable, the atmosphere would need to change. The Solonians, meanwhile - a dispossessed, outcast people led by a man named Ky - wanted to petition for independence, but their efforts were hindered by the Marshal of the skybase, who wanted to keep Solos under his rule so that he would continue to have a job. And the planet itself was beginning to be rocked by firestorms, in which blazing balls of fire rained down from the sky. While these only lasted a few minutes at first, their duration grew and grew until they lasted the entire night. And after each firestorm, the average temperature on Solos grew warmer. Strange things began to happen to the soil and the plants, as well as the atmosphere.
The Marshal wants to continue with his plan to make the Solonian atmosphere breathable for humans, and he plans to do this by bombarding the planet with ionization rockets which will seed the atmosphere with ionization crystals. As a side effect, this will kill all the Solonians (although they seem perfectly capable of breathing an Earth-type atmosphere and could presumably be relocated temporarily), but the Marshal considers the natives to be thorns in his side and would not mourn their loss. His experiments toward this goal seem to have precipitated the firestorms that bombard Solos.
Meanwhile, to the Marshal's outrage, more and more mutations are beginning to appear among the Solonian populace. Their arms or spine seem to change first, and they hear a voice telling them to go to the Place of Sleeping, the Place of Darkness and Light. Gradually their entire bodies change until they look like a large ant-like creature, with large claws, big eyes, dangly mouth-tentacles, chitinous skin, a ridge along the spine and an ant-like abdomen protruding behind their legs. They tend to lumber along, they growl, and sometimes they even speak, but they are afraid of fire and can be kept at bay with it. Generally they are harmless, because they run away when approached, but they can be dangerous. Much like other animals, as their numbers increase, so does their aggression. The Earthmen try to deal with them by sealing them into the caves and suffocating them with gas.
The Time Lords send the Doctor to Solos carrying, in a sealed message box, tablets that bear ancient Solonian writings that no-one still understands, from the culture that existed before Earth's arrival. The symbols match the hieroglyphs found in old temples on the planet, and with the help of Sondergaard, who had gone into hiding in some of the caves, the Doctor is able to decipher them. The tablets tell the story of how Solonian civilization began. Because the planet does not tilt on its axis, there are no traditional seasons; instead, because Solos takes 2000 years to circle its sun, its seasons can be divided into 500-year segments. The Earth colonists arrived at the beginning of the Solonian spring, and now the planet is segueing into summer. During the summer season, the planet is infused with radiation, like that found in certain parts of the caves, causing mutations. The Solonians, then, change with their environments, and while the mutations are natural, the Marshal's experiments have accelerated them unnaturally. Theirs is a kind of adaptive metamorphosis, in which the mutts should be an intermediate stage. The Doctor and Sondergaard also find a mysterious crystal in one of the most radioactive chambers, but it seems to have no radioactive properties. Once this mystery has been solved, Sondergaard goes to talk to the frightened mutants and explain the situation to them.
The Doctor then attempts to stop the Marshal's experiments, but too late; the Marshal launches his ionization rockets prematurely, leading them to malfunction and explode on the surface instead of the atmosphere, creating a lethal desert on the planet's surface. The Doctor is able to correct the ionization using particle reversal, but to guarantee his compliance, the Marshal keeps Jo and Ky locked up in a radioactive chamber powered by the mineral thaesium, found on Solos. With the Doctor's mysterious crystal present in the room, Jo finds out first-hand that the crystal acts as a biokinemetic agent; when combined with thaesium radiation, it causes the mutation. Ky swiftly transforms from a humanoid into a mutant, and then into a rainbow-hued glowing being. This new lifeform can float, pass through walls, and dematerialize; it can also emit a golden beam that has the power to paralyze and vaporize.
The Marshal plans to turn Solos into New Earth by any means possible, even if it means imprisoning the crews of visiting Earth ships on the planet; but the Doctor overloads his ionizing machine, and Ky, as a new Solonian lifeform, deals with the Marshal himself. The Doctor concludes that because the mutations were triggered too soon, their instincts were too confused to seek out and use the crystal. Sondargaard and Ky return to Solos to help the mutants transform into their next phase of life. Eventually, they become widely established in the Cyclops Nebula.
