After taking the kidnapped Earthling back home, the Doctor orders K9 to set a course for Gallifrey. He claims to be looking forward to seeing Leela and Andred again, but realises that Romana is upset about having to return -- for she only joined him in the first place to help search for the Key to Time, and she knows that the Time Lords now want her back. She has learned so much in her time with the Doctor that the thought of returning to the stifling life of Gallifrey appals her, but it appears that she has no choice. As the TARDIS approaches Gallifrey, however, it passes through a spatial anomaly which K9 is unable to interpret. When the ship materialises the scanner shows the wilderness of Outer Gallifrey -- but when the Doctor and Romana step out of the console, they find themselves in a pine forest. The co-ordinates are set for Gallifrey and the scanner persists in showing Gallifrey, but they've landed on the wrong world.

Elsewhere, as laughing youths swim in the river, a group of Outlers who have rejected the community try to steal the riverfruits they need to survive. Driven away from the banks of the river by the angry citizens, the young Outlers return to their cave, where their leader, Varsh, is surprised to see his young brother Adric. Adric is fed up with the regimented life of the starliner and wants to join the Outlers -- but when pressed, he admits that he has an odd feeling that when the starliner leaves Alzarius he will be neither on the ship nor the planet, but somewhere else. The others, Tylos and Keara, are put off by Adric's unconscious arrogance, and mock his pride in his gold star, a badge he earned for mathematical excellence. In turn he mocks their inability to steal riverfruit, and the angry Tylos challenges him to prove his worth to the Outlers by stealing the riverfruit themselves. Despite Varsh's objection, Adric accepts the challenge.

The leaders of the starliner community have far more pressing concerns than the Outlers. The scientist Dexeter has confirmed that recent riverfruit harvests are contaminated with insect eggs -- and First Decider Draith reluctantly confirms that these are indeed signs of a disaster soon to befall their community. Much as he would like to unburden himself of the secret knowledge of the System Files, however, he is unable to go into any more details. He and Dexeter return to the riverbank to conduct further tests, but these prove unnecessary, for as they watch the river begins to bubble, patches of fog bursting from beneath its surface. Within seconds a cloud of mist is rising from the river and marsh, and Draith has no choice but to announce the coming of Mistfall. The citizens are alarmed, but do not panic, for they know the procedure; they have two hours to collect everything they can and evacuate into the starliner.

Adric tries to take advantage of the confusion to steal some of the riverfruit, but Draith notices him and, enraged, pursues him into the forest. He runs Adric down by the river's edge when Adric falls and cracks his knee open on a rock, but Adric still refuses to return to the starliner, and as they struggle Draith slips and falls, knocking himself out. As Adric tries to revive him, something grabs Draith and drags him into the river -- and the struggling Decider's last words are to "tell Dexeter we've come full circle!" Meanwhile, Varsh, Tylos and Keara return to their cave to find that they are the only Outlers remaining; the others have panicked and fled back to the starliner. Varsh had always believed that Mistfall was a myth invented by the Deciders to strengthen their hold over the community, but it's real -- and if everything they say about it is true, then the Outlers are as good as dead already.

As the frightened citizens file into the starliner, the prominent citizens Login waits anxiously for news of his daughter Keara. Soon the mists will grow too thick for the air to support life, and the doors will be sealed, leaving everyone outside to their fate. Deciders Nefred and Garif cannot alter the law, even for Login; they cannot even wait for Draith to return. Time runs out, and as the deserting Outlers rush into the starliner with seconds to spare, Login must watch in despair as the airlocks are sealed, condemning his daughter to death. Despite his loss, he vows to redouble his efforts towards the Embarkation, and Nefred and Garif, knowing that they must choose another Decider to replace Draith, decide that Login should be the one.

Adric, limping terribly and unable to get back to the starliner, stumbles across the TARDIS instead. As the Doctor and Romana tend to his injury, he babbles about what he's seen, and at first they assume that he is hallucinating. He soon recovers, however, and when he takes in his surroundings and describes the exterior of the TARDIS perfectly, the Doctor realises that he's telling the truth. The Doctor decides to investigate, as there's nothing more he can do with the console -- and he's beginning to suspect that the scanner is showing an accurate picture in any case. The scanner's image translator interprets the absolute values of the exterior co-ordinates, and whatever the TARDIS passed through may have caused them to materialise somewhere with negative spatial co-ordinates... which would mean that they are no longer in their own Universe. Soon after the Doctor and K9 set off, Adric decides that he's recovered enough to get to the cave and warn the Outlers. Romana gives him a homing device so he can find his way back to the TARDIS -- and is surprised to see that his knee has already healed perfectly.

The Doctor and K9 take shelter as the Marshmen stride up the banks of the river, and watch as they pause, taking deep sucking breaths of air. They seem to be acclimatising to their new environment -- and doing so surprisingly quickly. Eventually they stride off, and the Doctor orders K9 to follow them while he heads back to the TARDIS. Before he can leave, however, a Marshchild rises from the swamp before his eyes, and although he tries to approach it peacefully it panics at the sight of him and runs away.

Adric returns to the cave to warn the others that the legends are true, and that Draith was dragged into the swamp before his eyes. He gives Tylos Romana's homing device as proof of his claims, but this proves to be a mistake -- for the Outlers need somewhere to shelter, and now Tylos can find the TARDIS without Adric's help. The Outlers locate the TARDIS, surprise Romana and overpower her, and announce that they are taking over her ship; but when Tylos threatens Romana, demanding to know where the Doctor is, Adric won't tolerate this and surprises him, knocking the knife from his hand. Romana picks it up... and returns it to Tylos, who is too surprised to threaten her further. But before she can leave to search for the Doctor, the TARDIS begins to quake and the occupants are flung about -- as if something had picked up the ship...

Unaware that he is being followed by the curious Marshchild, the Doctor returns to the TARDIS -- or rather to the place where the TARDIS used to be. All that remains is an indentation on the ground. Puzzled, he sets off to search for it, but finds the starliner first. A quick pass with the sonic screwdriver gets the Doctor through the main airlock and into the starliner's entrance hall, and after a quick look through the record books and a brief scout around the corridors in search of life, he seals the airlock behind him and sets off to explore. He is unaware that in the brief period while the airlock was open, the Marshchild entered and is continuing to follow him...

Nefred is now the First Decider, and he now carries the crushing burden of the knowledge contained within the secret System Files. Login accepts his and Garif's offer to become the new Third Decider, and life in the community carries on. Although they are now sealed within the starliner, the citizens know that they must continue their work towards the Embarkation, as they have done for generations ever since the starliner first crashed on Alzarius. A citizens' work detail finds the Marshchild aboard, however, and when they attack it the Doctor intervenes, realising that the Marshchild is just as frightened of them as they are of it. The hostile Omril, realising that the Doctor must have opened the doors to let it in, drags him off to the Deciders while the struggling Marshchild is taken to Dexeter for study. The Doctor answers the Deciders' questions as best he can, and Login is stunned when the Doctor casually mentions that the mists are non-toxic -- and Nefred and Garif confirm that this is a myth spread to keep the citizens from venturing outside during the dangerous Mistfall. As Login realises that his daughter might still be alive, Dexeter arrives to announce that the Marshchild shows none of the characteristic aggression of the species, and is therefore useless to him. The Doctor, however, offers a second opinion.

Dexeter has anaesthetised the Marshchild and has been taking tissue samples, driven by his desire to learn all he can about the Marshmen before the starliner leaves Alzarius. The Doctor isn't terribly interested by the remarkable regularity of the Marshchild's cell structure; he's more interested in getting the Marshchild and himself back to their natural habitats. Login offers to help the Doctor leave the starliner and find his missing TARDIS if the Doctor agrees to help find Keara. As they approach the airlock, the Doctor catches sight of a repair team replacing what appears to be an image translator; it isn't, but to his surprise the team is replacing a fully functional optronic circuit. Login is vague about the details, but assures the surprised Doctor that everyone in the starliner accepts that it may take generations to repair the damage.

The airlock is now being guarded, and Omril refuses to reopen it. Login is about to exercise his authority as a Decider when the TARDIS unexpectedly materialises in the boarding zone. At first, the Doctor assumes that Romana has piloted it here, until the confused Outlers emerge. The Doctor bustles Adric back inside and departs, demanding to know what's happened to Romana, while Login is joyously reunited with Keara. There must be an inquiry into their actions, but Login uses his authority to plead for the Outlers' case; they may be rebels, but they are rebellious children, and they now understand the truth about Mistfall and that the Deciders work for the good of the community. There will be no punishment; the Outlers will be allowed to rejoin the community and to work towards the Embarkation.

The Doctor short-hops back to the cave, where he and Adric find the headless remains of K9, a dead spider and the dazed Romana, who doesn't seem to recognise the Doctor. Moments after entering the TARDIS she collapses, and the worried Doctor decides to analyse the spider's remains in Dexeter's laboratory and find out what has happened to her. But back on the starliner, the Marshchild is awakening, and Dexeter intends to operate upon its living brain to find the answers he seeks about the species' behaviour. Nefred, clearly conflicted by his private knowledge about the System Files, authorises Dexeter to conduct the operation -- but orders him to do so in secret while the Deciders observe. The Doctor arrives in the Great Book Room with Adric to see Dexeter on the monitor screen, preparing to cut open the Marshchild's living brain. Furious, he demands that Dexeter stop what he is doing, but the scientist proceeds -- and is taken aback by the ferocity with which the Marshchild responds. Within seconds it pulls free of its restraints, kills Dexeter and smashes apart the laboratory. It then sees the Doctor's face on the science unit's viewscreen -- and as the Doctor watches helplessly, it punches through the screen to get to him, and electrocutes itself.

Enraged, the Doctor sends Adric back to the TARDIS and then lays into the Deciders, blaming them for the deaths -- and for the fraud which they have committed upon the community. To Login's horror, the Doctor pulls the manuals from the shelves of the Great Book Room to reveal fully functioning navigational and control systems; the ship has been ready to take off for centuries, and the Deciders have kept this secret, perpetuating endless and pointless repair work. The Doctor believes they have done so to maintain their power over the community... but Nefred reveals what no Decider had dared to admit before now. The manuals in the Great Book Room contain complete schematics of the ship, and if the people so wished they could take it apart and put it back together down to the smallest rivet. But nobody knows how to pilot it.

The Marshmen spread out through the starliner, armed with makeshift clubs. The Outlers' maintenance team is in the boarding zone when the Marshmen arrive, and Varsh flings his satchel of spare parts over the floor as a distraction. The Marshmen study the objects curiously, as if trying to work out what they are for, and the Outlers flee -- but Tylos remains to rescue their foreman, and is himself caught and killed as the foreman flees for his life.

As the Doctor and Adric search for Romana, a chance remark of the Doctor's reminds Adric of Draith's final words -- that they'd come full circle. When the Doctor notices that Adric's knee has been healed for hours this supports his dawning suspicions, but before he can return to the Science Unit he and Adric learn that the Marshmen are aboard. They are reunited with the fleeing Varsh and Keara, and the Doctor sends them back to the Science Unit while he returns for Tylos. He finds Tylos' body lying by the TARDIS, and is confronted by a Marshman wielding the head of K9 on a club. The Doctor snatches it back, but is then confronted by the mutated Romana. Realising that the alien proteins in her bloodstream are affecting her brain, he shows her the TARDIS, and as she runs her hands along the outside, trying to remember why it's so familiar, he returns to the Science Unit, hoping to find a cure -- and a solution to the larger problem.

The citizens evacuate into the Great Book Room, where Login tries to organise them to find a solution; but Nefred and Garif waffle uncertainly, claiming that their research proves that the Marshmen will adapt to any tactics devised against them. As they leaf through the manuals, seeking answers there rather than trying to think up solutions of their own, Login realises that they have been stuck in procedure for too long to cope with this crisis. The Marshmen break into the Great Book Room, and although Login manages to organise an evacuation while the Marshmen tear apart the manuals, Nefred is struck down and seriously injured while trying to flee. Login and Garif get him to safety in the inner hull and seal off the bulkheads, but the dying Nefred tells them to find the Doctor. He can teach them to pilot the starliner and take them away from Alzarius -- but they cannot return to Terradon. They have never been there.

The Doctor and the Outlers barricade themselves in the Science Unit, where the Doctor discovers that Adric has stolen the image translator from Dexeter's microscope as a gift for him. If it works in the TARDIS it will prove that they are in the Exo-Space/Time Continuum, but that's a problem for later. The Doctor repairs the microscope and analyses the spider cells, planning to synthesise a serum to cure Romana. As he does so, however, the Marshmen break in. The Doctor picks up a nearby oxygen cylinder to defend himself, and the curious Marshmen pick up further cylinders themselves. One of the Marshmen accidentally pulls off the valve, flooding the room with oxygen more quickly than even the Marshmen can adapt to it. As they flee out into the corridor, Romana enters and attacks the Doctor, but she cannot handle the rich oxygen content either and passes out. The Doctor gives her the serum, which will either cure her or kill her.

Varsh and Adric drive the Marshmen into the corridors with the oxygen cylinders, and meet Login and a party of citizens seeking the Doctor. As they pass through the boarding area, however, more Marshmen emerge from the ventilation ducts, and Adric and Varsh hold them off while the citizens flee to safety. Adric's cylinder runs out of oxygen, and Varsh remains to hold back the Marshmen while Adric rushes back to the Science Unit for more. Meanwhile, Romana recovers and helps the Doctor to analyse the cell samples from the spider, the Marshchild and Dexeter -- which are all identical. According to Keara the starliner crashed on Alzarius 40 generations ago, but the Doctor now knows that it happened much longer ago than that. Adric rushes in to collect a cylinder and heads back to the boarding area, but he is too late; Varsh's cylinder has also run out, and he has remained to close the bulkhead while the others get to safety. Adric is just in time to see his brother being pulled beneath the descending bulkhead by the Marshmen, and by the time he raises the bulkhead again, the Marshmen have gone and his brother is dead. Keara gives Varsh's marsh reed belt, the symbol of the Outlers, to the grieving Adric.

The Doctor consults with Login and learns that the starliner has an electrolytic power source, capable of flooding the corridors with oxygen. Login gives the order to do so, and soon the Marshmen are forced out. The Doctor stops Login and Garif from opening the emergency hatches, however, and makes them watch as the Marshmen claw about the edge of the hatch -- and then locate the opening mechanism and learn how to operate it. They are intelligent, inquisitive creatures, and given time can adapt to any environment -- just as they did generations ago, after wiping out the original crew and passengers of the starliner. The people of the starliner community are Marshmen themselves, who began to live in the wreckage of the starliner and eventually evolved into forms more suitable for that environment. This seems to be what the Marshmen cannot tolerate about them... and now that they have learned how to get out of the starliner, what's to stop them learning how to get back in?