The TARDIS materialises in an underground tunnel and when the Doctor and Charley emerge, they find themselves overwhelmed by loud noises coming from nearby machinery. The Doctor thinks it sounds like a pressure generator unit, which suggests they’re on a planet that doesn’t have it‘s own atmosphere. The caves are clearly man-made and the Doctor recognises the technology as human, similar to that used in the Moon conurbations of the late 30th century. As they move off to explore, a man emerges from the shadows and uses his com-link to contact a woman to tell her about the new arrivals. He warns her that there’s going to be trouble when security find them…

The Doctor and Charley soon realise the tunnel is heading upwards, but this is good news as they should be able to tell where they are once they reach the surface. Charley is quite looking forward to seeing the Moon as she’s never been there before - a fact which doesn’t surprise the Doctor, although he finds it odd that she should mention it so casually - but he promises to get her home one day, wherever that might be.

The colony has been mining on the planet Onyakis for a year now and all Commander Rag Cobden has to show for it is a pile of reports full of disappointing results. The amount of the K-7 crystal mined so far is just 5,000 metric tonnes and their initial hopes of exploiting its energy yielding properties were soon dampened when their experiments showed it to be inert. He’s therefore shocked when he receives a visit from Professor Lyle Woodruff who tells him they’ve had a response at last. He says his people were taking a look at one of the artefacts Rob Harvey’s team found and they‘ve got a power reading. At first, Cobden is angry as he didn’t give permission for the test, but when Woodruff tells him a sample of the K-7 reacted to the artefact, they rush off to the laboratory to see for themselves.

The Doctor and Charley arrive at a set of big metal doors leading to an observation gallery. The Doctor gets to work on opening the blast doors, but it’s not easy as everything is covered in rust. A man joins them and says the doors haven’t been opened for months as no one’s interested in seeing the surface these days. He introduces himself as service technician Daniel Romilly and gives the doors a hefty kick, which does the trick. The doors open to reveal a landscape not dissimilar to the Moon, only purple, and in the sky above are two enormous colony ships bearing the logo of Euro Comgen. Romilly assumes the two visitors have just come down from the ships on the shuttle, but then another man arrives with a gun and demands to know what they‘re doing here…

Woodruff takes Cobden to the laboratory and is about to switch on the equipment when a call arrives from security for the Commander. They’ve just discovered there are two intruders in the tunnels - a man named Ned Gillespie and a woman named Eleanor Harvey - who’d used faked name tags to get past the scanners. Cobden thought Gillespie had been marked for re-cryo after his last protest, but it turns out he’s awaiting a hearing after lodging an appeal with the council. When Cobden learns that Eleanor is the mother of Rob Harvey, he’s shocked and gives immediate orders for the two to be buried…

The man with the gun, Ned Gillespie, tells the Doctor and Charley to get back to their ship before they land themselves in trouble. He doesn’t believe their story that they’re from Earth as all life there was destroyed centuries ago. The Doctor recalls his earlier visit to Nerva and realises they’re in the time of the solar flares, which explains the colony ships above them. Romilly explains that the solar flares all happened a long time ago. They’re on Onyakis and there isn’t another habitable planet for light years around.

In the laboratory, Woodruff asks Cobden to put on an old-fashioned headset. He says his team has discovered thousands of artefacts, each of which has headsets like these built into them. He thinks they’re some kind of teaching machine because when you put the headset on, problems start popping into your head and when you think of the solution, you feel good about it, as if someone is pleased with you. The Professor produces a sample of the crystal K-7, a beautiful geometrical solid which the miners call ’ice’ because it looks like a diamond, but then he produces another sample of the crystal which transformed into a liquid after he put on the headset and answered some of the questions. Cobden excitedly asks if it released any energy and the Professor says there was a massive discharge.

Romilly explains that the two Euro Comgen ships contain the sole survivors of the human race. The Doctor assures them they’re wrong, but Gillespie is convinced the humans aboard Nerva wouldn’t have stood a chance. The Euro Comgen ships have carried generations of humans here through the centuries, looking for a new home. Charley says the fact that they don’t have electronic identity implants, which are given at birth to everyone, is proof that she and the Doctor aren’t from here. Gillespie starts to get angry again and the Doctor criticises him for being suspicious of everyone - even the colony leader Cobden - and of skulking around in the dark and threatening people. He’s also realised that Gillespie is a hunted man and a crusader, and he offers to help if they can explain exactly what it is that Cobden has done wrong. They’re interrupted by the arrival of a security truck and Gillespie accuses the Doctor of deliberately keeping him talking to give the guards time to home in on him. He tries to contact his colleague Eleanor, but gets no response and realises the guards must have caught her already. The security truck screeches to a halt further down the tunnel and a voice calls out, ordering Gillespie to drop his gun.

Cobden seems oddly distracted, so Woodruff suggests he take off the headset for a while, especially as they don‘t know whether there‘ll be any side effects. The Commander angrily resists and says he doesn’t want to take it off, but when the Professor receives a call from security to say that Gillespie was accompanied by two strangers who claim to be off-worlders, he has no choice but to forcibly remove the headset. Cobden seems confused for a moment, but then he sees the Doctor and Charley on the scanner and becomes hostile. The Doctor asks him why they chose Onyakis as it seems far from ideal as a colony planet and learns that most of the colonists are still in cryogenic suspension aboard the ships. Gillespie interrupts and demands to know what’s happened to Eleanor’s son Rob. The technician Romilly has also been arrested, although he argues that he was just caught up in this while trying to do his job. Cobden has heard enough and switches off the com-link. The Doctor realises there’s something not quite right about the Commander and thinks he recognises the strange look in the man’s eyes. Gillespie says that although their job here is to safeguard the colony Sleepers and look for planets with raw materials and fuel, Cobden rides rough-shod over the council and breaks all the rules.

Woodruff shows Cobden what’s left of the second sample of K-7 and confirms that the transformation took place while he was connected to the teaching machine. Cobden wants to continue the experiment while Woodruff finds a way to harvest the energy released. He believes this is the power source his people have been looking for all this time and it will ensure their survival.

The security truck goes deep into the lower levels of the planet and eventually comes to a halt. The guards open the doors but leave the prisoners to climb out themselves. They emerge to discover they’re no longer in one of the mining areas. Eleanor tells the Doctor her son Rob was among the first miners to come down here, but then he “disappeared” and it seems clear Cobden is responsible somehow. Gillespie says they came to Onyakis over a year ago to mine the K-7 after they picked it up on a long-range scan two systems away. It was going to be the answer to all their problems, but it hasn’t worked so far and people are starting to suspect Cobden faked the evidence. If that’s true, the miners have collected several thousands tonnes of the crystal just for the sake of propaganda. An idea is starting to form in the Doctor’s mind…

Cobden puts the headset back on and Woodruff can see that something is starting to form inside the K-7 liquid. The security guard contacts them again to say the prisoners are in position and that they’re waiting for the word. Cobden seems confused, but eventually he tells them to do it…

The security truck drives away quickly, leaving the Doctor, Charley, Gillespie, Eleanor and Romilly alone in the dark tunnel. Eleanor accuses Gillespie of using her son’s disappearance as an excuse to pursue his own agenda, but Gillespie insists that he discovered that Rob had learned something Cobden didn’t want made public. The rumour is that K-7 has something to do with an alien life form, which would put a halt to the mining operation as the council rules state that any trace of civilisation must be investigated first by their xeno-archaeologists. Cobden would do anything to cut through the red tape - including arranging for young Rob Harvey to disappear. It suddenly occurs to them that they’ve also been put down here to “disappear”…

The security team come to a halt a safe distance away and proceed with the planned “demolition”. A switch is activated and the entire tunnel is shaken by a tremendous explosion, which fills the entire area with clouds of dust and falling rocks. The chief officer contacts Cobden to confirm the job has been done and the Commander regrets another “unfortunate cave-in”. Woodruff says he thinks they should stop their experiment in order to put some safety procedures in place, but Cobden refuses to listen. The formation inside the K-7 liquid starts to take firmer shape and Woodruff is horrified, but the Commander is delighted with the results and orders the Professor to leave…

In the tunnels, the dust starts to settle. The Doctor helps pull Eleanor from beneath some rubble and it looks like they may be the only survivors. He’s amazed they weren’t killed outright, but the rock fall has exposed some kind of huge structure that must have protected them from the debris. The Doctor recognises it instantly as a spaceship that‘s obviously been buried for a very long time. He uses Eleanor’s com-link to call the others and is relieved when Charley responds from the other side of the blocked tunnel. She’s with Gillespie, who’s alive but badly hurt, but there’s no sign of Romilly. Charley confirms that she can also see the alien structure above them which was uncovered by the explosion. The Doctor can see an entrance on his side, so Charley suggests she try to find another entrance on her side and then they can meet up inside.

The Doctor and Eleanor enter the spaceship and hear a strange noise, as if liquid is leaking from somewhere. They eventually find themselves in the main control room and the Doctor finds the area is filled with crystals which Eleanor confirms is the K-7. The crystals are unusually malleable, which surprises them as they remember Romilly said it’s like diamond. The room also contains hundred of machines, all lined up in a row, which again seems familiar to the Doctor. When Eleanor points out that they all have headsets attached, he switches one on and it starts to communicate with him via a form of telepathy. Then the machine sets a problem for him…

Cobden screams in protest when Woodruff tries to physically remove the headset from him. Weakly, he insists on being allowed to continue, but the Professor points to the “thing” that the learning machine has created. He approaches the huge crystalline figure and cautiously asks it if it’s alive and whether it can understand him. The Kroton responds by pointing to Cobden and informing him that the High Brain is exhausted. It orders Woodruff to put on the headset and continue the process in his place…

The Doctor tells Eleanor he’s seen the Kroton teaching machines before, but these are more advanced and sophisticated, and the running water they heard earlier is all that remains of the K-7 deposits. Charley contacts him to say she’s found a way into the ship, but it’s a bit of a climb. Just then she finds Romilly, who appears to be unhurt if a little dishevelled. He too notices the sound of water and they soon realise the entire place is flooding. The Doctor tells them the liquid is a hostile crystalline lifeform in flux and they need to get inside the spaceship as quickly as possible. Charley tells him they’ll have to climb up a fairly steep rock face and it’s going to be difficult for Gillespie who has an injured leg. Before the Doctor has a chance to warn them, Romilly sticks his hand into the liquid, but there don’t seem to be any ill effects. Together, he and Charley lift Gillespie to his feet and help him towards the spaceship entrance above them.

The Doctor can’t understand why the K-7 is still liquefying even though he’s stopped using the teaching machine, but then he realises Cobden must have been using one of the machines too and it‘s the power he’s creating that’s transforming the crystals here. Below Charley, Romilly and Gillespie, the pool of liquid on the floor starts to boil. The liquid then starts rising and they can feel the heat coming off it. As they struggle to keep away from it, Romilly loses his grip on the rock wall and falls away, instantly disappearing beneath the liquid. Charley wants to go back down to help him, but it’s too late and there’s nothing she or Gillespie can do to save him.

The Doctor sadly confirms that Romilly wouldn‘t have stood a chance - in fact, it‘s likely he fell because the crystalline substance had already entered his system when he touched the liquid. He decides to contact Cobden and try to persuade him to stop whatever he’s doing. Eleanor is sure he’ll never speak to them personally, so she offers to call his office aboard the colony ship. She gets through to the communications computer, but it refuses to transfer her unless she explains the nature of her call. The Doctor says their intention is to expose Commander Cobden as a despot and a murderer, but the computer insists this is a matter for their security division. Instead, the Doctor asks the computer to look for unusual energy readings coming from Cobden’s location as the Commander is illegally using an alien machine that will destroy the colonists on both ships if he’s not stopped. The computer informs him that Commander Cobden is in Professor Woodruff’s laboratory, but again it insists on referring the matter to another department. While he’s waiting, the Doctor briefs his friends on the Krotons. He says they’re a parasitical crystalline lifeform that uses the mental impulses of sentient races to activate themselves and to power their technology. He adds that the boiling liquid Romilly fell into is a kind of primordial soup made up of the same substance as the Krotons. He believes this ship crash landed here centuries ago and when their power was exhausted, they reverted to their constituent form. In the meantime, his call to the security division is put on hold in a queue…

Charley and Gillespie are now inside the ship and are making their way down a walkway, but it’s still a struggle for them and they keep falling over. Gillespie becomes angry with himself and he tells the Doctor that Charley’s going to have to leave him behind as he can‘t go any further. The Doctor assures Charley it should be safe for now, but he warns them that Cobden is somehow releasing enough energy back up on the ship to continue the Kroton reactivation down here on Onyakis. Their inert dormant phase is already over and the primordial soup will eventually reconstitute itself into their active form. He tells them the Krotons are highly aggressive bio-mechanical crystalline entities and they view all sentient life as nothing more than a source of energy to be used up and discarded as waste matter.

In his laboratory, Woodruff is now at the point of complete exhaustion, but the Kroton orders him to continue as his mental energy is transmitting down to the planet to reactivate the other Krotons. Nearby, Cobden is starting to come round, but he’s extremely weak and still in a confused state. The ship’s computer alerts him to the fact that dangerous levels of unknown energy are being detected in his location and a security detail has been sent to investigate. The computer tells him someone down on the planet wishes to speak to him and he realises it must be the Doctor. The Doctor hears the Kroton try to stop Cobden, so he quickly yells out to tell him to switch off the learning machine as if he’s feeding it with his brainwaves. Cobden tells him it’s too late as they’re already moved on to Woodruff and he’s too weak to stop them. Cobden tries to explain his actions, but the Doctor accuses him of breaking the rules and using dirty tricks to get his own way - and by doing so he may well have brought about the destruction of the whole colony! When Cobden asks the Doctor how he can stop them, the Kroton advances towards him menacingly…

Inside the Kroton spaceship, the Doctor and Eleanor listen as Cobden screams, then the coms-link is broken off. The Doctor is furious with the ship’s computer for taking so long to put him through. Elsewhere on the ship, Charley calls the Doctor and says she can hear something mechanical moving nearby. He warns her that other Krotons must have become active by now. Just then, they hear the sound of Cobden’s security people forcing their way into the laboratory back on the Euro Comgen ship. Unfortunately the Doctor knows they won’t stand a chance…

The chief security officer squares up to the Kroton in the laboratory and orders him to release Professor Woodruff. The Kroton warns them to stay back and put down their weapons, adding that once this High Brain is drained, the officer will take his place at the machine. The security team opens fire and the air is filled with the sound of laser fire. When the noise has died down, the unharmed Kroton turns its own weapon on them and the group is dispersed within seconds.

Distracted by the sound of the slaughter on the ship, the Doctor and Eleanor are caught by surprise when another Kroton appears in the control room. The Doctor explains that the Krotons use a weapon that totally disperses living tissue on a molecular level and the effect is both very nasty and very final. Charley contacts the Doctor and tells him she and Gillespie are now surrounded by more than twenty of the creatures. He warns her not to resist as they won‘t take no for an answer. Charley reminds the Doctor that he’s met these creatures before, which means he must know of a way to destroy them, but he tells her the only thing they can do now is surrender!

Later, under the supervision of the Krotons, the two Euro Comgen colony ships descend from their orbit around the planet Onyakis and land close to the tunnels where the crashed spaceship was found. Orders are given for the first batch of humans to be taken to the learning chambers while the ‘non-human’ High Brain is brought back to the newly regenerated control room. The Doctor meets the Kroton leader and learns that the Dynotrope he destroyed on the Gond planet was an inferior form of craft and this group of Krotons are much more advanced. One thousand Krotons have already been reconstituted and they plan to use the Doctor’s superior mind to supervise the mental processing of all the remaining humans. He refuses to help, but the Kroton tells him his refusal will only delay their plans, not stop them, and as they’ve lain dormant here for three millennia, they’re in no particular hurry.

The Kroton reveals that their ship crashed here because of an energy failure and once they’re restored back to normal, they’ll continue with their plan to set up a chain of human outposts, all slave to their machines. Their aim is to establish a transference network that will power their ships wherever they go, allowing their influence to expand. Under threat of immediate dispersal, the Doctor is forced to help them. They tell him he can have the assistance of Charley as her mental processes show evidence of being recently expanded. They’re ordered to join another Kroton inside the primary unit chamber and put on their headsets. The Doctor and Charley notice there’s something different about this particular Kroton, then suddenly they realise there’s a human eye embedded on the other side of its head and there’s human flesh on the arm attachments. The Kroton turns to speak to them and they realise, to their horror, that it’s Romilly…

Moments later, Gillespie and Eleanor are accompanied by another Kroton into the primary unit chamber to join the Doctor and Charley. The Doctor is confused - he knows why he and Charley are needed, but he can’t understand why the other two have been brought here too. The Romilly-Kroton assures the newly arrived Kroton that he doesn’t require any assistance and once they’re alone with him, the Doctor explains to the others what’s happened to their former colleague. Charley and Gillespie saw him fall into the primordial soup and although it should have killed him, a chance in a million has resulted in some sort of hybrid. The Doctor tells them the other Krotons haven’t noticed anything unusual because they’re not very good at visual perception. Romilly admits that he had Gillespie and Eleanor brought here as he needs their help to defeat the other Krotons. The Doctor points out that there are probably thousands of them by now and they have the whole colony under guard.

Romilly tells the group to put on headsets, but while they decide whether or not they can trust him, an announcement is made throughout the ship alerting them to the commencement of the first phase. For the sake of appearances, the Doctor encourages everyone to do as Romilly says. He and Charley can immediately sense something, like an idea has popped into their heads, and the Doctor thinks it’s the Kroton equivalent of a computer programme. Romilly tells them if they activate the programme with their minds, it will destroy the other Krotons. The Doctor remembers that Romilly was a service technician, so he’ll know everything about the systems on the colony ship and here on the planet. Gillespie and Eleanor also start to see an image inside their heads and the Doctor realises they’re looking at the atmospheric pressure generator that the TARDIS landed next to. He now realises what Romilly intends to do and he pleads with him not to go ahead with his plan. The moment the mental energy starts to flow from all the teaching machines on this ship, the generator will start to build a super-dense atmospheric bubble throughout the tunnels. The explosion will probably kill them all, but even if it doesn’t, it’ll set Onyakis on a new orbital path directly into this system’s Sun. He believes Romilly has been driven totally insane by his experiences and he doesn’t understand that his plan will destroy everyone, not just the Krotons.

Just then the programme is initialised and the Doctor can sense the minds of thousands of humans, all slave to the machines in the hold of the Kroton ship. Romilly tells them not to fight against it, but one by one the group begin to cry out in agony as the effects of his programme take hold. An alarm sounds and the Kroton leader is informed that their power is being diverted. He suspects the Doctor is interfering with their plan and gives orders for him to be dispersed immediately. When the Krotons enter the primary unit chamber, Romilly opens fire on the leader, killing him instantly. The Doctor urges everyone to take cover as a full-blown battle ensues in the chamber. Eventually the Krotons, including Romilly, destroy each other. With great effort, the Doctor manages to release himself and heads for the atmosphere generator.

Charley uses the com-link to guide the Doctor through the tunnels to his target. Fortunately he stumbles across one of the abandoned security trucks and uses it to drive the rest of the way. Before long, more Krotons arrive at the primary unit chamber and accuse the humans of destroying their leader. Charley says that if she stops using the learning machine, their power will start to drop, but the Krotons already know that it’s being diverted and is no longer regenerating their ship.

The Doctor arrives at the atmosphere generator, but when he tries to contact Charley again, he gets no reply. As he enters the control room, he hears the voice of the Krotons over the com-link. He starts shutting the equipment down and everything in the mine immediately stops working. He’s stopped Romilly’s plan, but unfortunately it also means no more air is being pumped out and everyone will soon start to suffocate. The Krotons manage to repair the error in the programming that Romilly created and they order the humans to continue regenerating their ship. They also instruct the Doctor to reactivate the atmosphere generators in order to keep Charley and the others alive, but Charley tells the Doctor not to listen to them. If the Krotons get what they want, what’s left of the whole human race will be connected to the machines and left to die.

The Doctor is faced with a dilemma - the only way to save the human race is to let Charley and the others die. Then he realises there’s something else he can do. Seconds later the generator is switched back on and the Krotons tell Charley, Gillespie and Eleanor they must continue with their work. The Krotons arrive at the atmospheric generator unit and order the Doctor to step away from the controls. He assures them they have nothing to worry about and says he’s set everything to maximum output.

In the primary unit chamber, the Krotons confirm that everything is running normally again. Charley and the others start to mock the Krotons and they refuse to be cowed by any threats made against them. They realise they can say anything they like because the Krotons can’t kill them or remove them from the machines as they’re needed right where they are. They start to get ever more confident and even begin taunting their captors, then the conversation becomes hysterical and Charley, Gillespie and Eleanor laugh uncontrollably. The Krotons realise there’s a problem and the humans assume it’s because their minds are simply too powerful for them. The power levels start to fluctuate and the heads of the Krotons begin spinning faster and faster until they eventually explode. Before long, all the Krotons are dead…