The Seventh Doctor takes Ace to the Museum of the Tellurian Stain (not Strain; history has not been kind to humanity) to see some of her species’ achievements. Ace’s curiosity is piqued by an exhibit about philanthropist Stewart Ransome, who set off from 25th-century Earth to found a colony on the planet Axista Four based on the “Back to Basics” philosophy proposed by his daughter Kirann. Ace wants to visit the colony in person, but the Doctor claims he’s been there already and doesn’t want to return. As the frustrated Ace sets off to search the TARDIS for the 500-year diary which the Doctor had casually mentioned, the Doctor, his own curiosity piqued, fetches the diary from its hiding place and begins reading, refreshing his memory about his second incarnation’s adventure on Axista Four.

100 years have passed since the Big Bang crashed on Axista Four. The “Back to Basics” creed forbids the colonists from using genetic engineering to help their crops grow in alien soil, and the colony is thus struggling to survive. Faced with a harsh struggle for existence, many of the original settlers’ descendants don’t wish to be held back by the artificial rules decided upon by their parents and grandparents. Some years ago, a breakaway group who call themselves “Realists” founded their own village some distance away from Plymouth Hope City, and there’s still a great deal of bitterness between the factions, especially as the Realists often must raid the “Loyalist” settlement for supplies. Four years ago, the son of Plymouth Hope’s sheriff Tam Kartryte was killed in a Realist raid, and he’s had to raise his grandson Billy Joe ever since. But Billy Joe believes that his father was trying to join the Realists that night and was caught in a crossfire. After a particularly bitter argument with Tam, Billy Joe runs away to join the Realists himself. However, as this is Planet Fall Day, the town is thronging with people, and Billy Joe, unable to steal a horse without being noticed, decides to shelter for the night in the forbidden wreck of the colony ship.

The Realists have established their community in the base of the mountains, 30 kilometres away from Plymouth Hope, in the ruins of an alien settlement. In the nearby caves, the scientist Max Forde has found a bunker of aliens in suspended animation; unlike the human colonists, who slept in cryogenic capsules for their journey, the aliens’ metabolism is slowed by the use of symbiotes attached to their bodies. Max is trying to wake the aliens so he can communicate with them, but his lover, Hali Devine, is more concerned with keeping her people fed, and she thus leads a party of Realists to the colony ship for more supplies.

Meanwhile, the Earth Colony Support Vessel Hannibal enters orbit, apparently in answer to a call the Realists sent some time ago. First Officer Veena Myles is aware that Major Jonn Cartor’s approach to sorting problems out is to bang heads together, but she’s surprised when Cartor awakens their other “guest”, Administrator Greene, from suspended animation. They are as yet unaware that their approach has been detected by a ring of disguised defence satellites. A century of disuse has depleted the satellites’ pulse weaponry, and the satellites thus send an emergency alert signal to the planet. The aliens in the bunker beneath the Realist compound receive the signal and begin to revive...

The TARDIS materialises in the wreck of the colony ship, and the Doctor is separated from Jamie and Zoe when he falls through a rusting part of the hull while exploring. While searching for a safe way down to the next level, Jamie meets Billy Joe, who is at first unsure whether to trust him but decides to do so when Jamie saves him from falling through another rusting hull plate. Billy Joe offers to lead Jamie back to his friends, and on the way, they find a sealed panel which Jamie inquisitively tries to open. He fails, but fail-safe mechanisms detect his interference and send out a battledroid to investigate. The battledroid finds and attacks the Doctor and Zoe, but the Doctor uses his sonic screwdriver to shut it down and wipe its short-term memory. As it retreats, the Doctor notes that there are several more sealed panels on the ship, and wonders just how many battledroids are lying dormant in the wreck.

One of Plymouth Hope’s most vocal troublemakers, Val Freedom, has disagreed with Tam Kartryte several times in the past, and has repeatedly advocated waking Kirann Ransome from cryogenic stasis to help them solve their problems. However, most of the colony’s medics were killed in the crash, and nobody now alive has the expertise to revive anyone from cryogenic suspension; thus, Kartryte rejects his suggestion. Frustrated, Freedom retreats to tend to an illegal still hidden in the restricted zone around the colony ship, and hears voices within the wreck. Believing that the Realists have mounted another raid, he alerts Kartryte, and despite their differences they badn together a posse to drive the Realists off their land.

The Doctor and Zoe are reunited with Jamie and meet Billy Joe, but the posse then arrives and attempts to arrest them -- just as Hali and her party arrive. Confusion breaks out, and in the resulting exchange of gunfire, Jamie and Billy Joe flee with the Realists while the still somewhat drunk Freedom shoots Zoe. Furious, the Doctor demands that Kartryte give his friend medical attention, and Kartryte agrees to do so but jails the Doctor until he can explain his presence. Once he and Freedom have questioned the stranger, however, they accept his claim to be an innocent traveller, and agree to release him and help him find his missing friend Jamie while the town healer, Dee Willoughby, tends to Zoe.

Jamie and Billy Joe are also questioned by the Realists, but while they accept that Billy Joe genuinely wishes to join them, they are more suspicious of Jamie. Unsure whether he can be trusted, they decide to lock him up in one of their pre-fabricated huts until they can question him further. They are unaware as yet that a more immediate threat comes from the alien bunker, where the Tyrenian commander Lorvalan and his second-in-command, Zenig, have just woken from 100 years of suspended animation -- to find that the enemy humans have apparently discovered the bunker. Lorvalan and Zenig set off to check the condition of their ship, intending to assess the current situation before taking military action, but action is forced upon them when Security Chief Dyselt also awakens, suffering from “Intelligence Reducing Virus” due to an illness in his Alisorti symbiote. The smell of humans in the bunker drives Dyselt into a primitive rage, and when Lorvalan and Zenig return, they find that the animalistic Dyselt has stolen a transport sled and set off hunting for humans, threatening to rob the Tyrenians of the element of surprise.

Kartryte decides to trust the Doctor and releases him, but as the Doctor explores the town he concludes that the “Back to Basics” philosophy is slowly killing the colony. Though Zoe seems to be recovering, the medical centre is nevertheless full of useful medical equipment which has been left to gather dust. Dee admits that many people in the colony suspect that the original philosophy had more leeway, but since Stewart Ransome died in the crash and Kirann remains in suspended animation, they have no way of knowing.

Cartor and Veena then arrive from the Hannibal, making a deliberately ostentatious pass over the town to catch the colonists off-guard. The Doctor convinces Kartryte and Freedom to let him accompany them to the shuttle, where Cartor reveals that the colony is about to lose its precious independence. Several frontier Earth colonies have recently fallen to a warlike race called the Daleks, and thousands of refugees are now searching for new homes. Due to the state of emergency, Axista Four is going to have to accept an influx of new colonists, none of whom agreed to the “Back to Basics” philosophy of the original colony.

As the shocked Kartryte and Freedom prepare to return to Plymouth Hope, the Doctor asks Cartor to have his ship’s medics look Zoe over, as he doesn’t entirely trust the colony’s primitive medical facilities. As he’d feared, the request alienates Kartryte and Freedom, who leave the Doctor behind and return to the city alone -- only to see smoke rising from the medical centre. Dyselt has arrived and attacked the building with the red cross, which reminded his addled mind of a targeting sensor display. Dee passes out from smoke inhalation without getting a good look at the attacker, and when Tam enters the building, furiously expecting to find Realist raiders, he is attacked and savagely mauled by Dyselt. Dyselt makes his escape as the Doctor and Veena arrive, and while Veena arranges for the grievously injured Kartryte to be taken to the Hannibal for treatment, Freedom realises, to his horror, that he’s just become the acting sheriff of Plymouth Hope.

The citizens believe that the Realists are responsible for the attack, but the Doctor isn’t so sure -- and when he examines the hospital, he finds evidence that the attacker may not have been human. He also finds Zoe, who had recovered before the attack but was then forced to hide in a disused cryogenic capsule. Cartor and Veena agree to use the Hannibal’s facilities to revive Zoe, but the Doctor is disturbed by Cartor’s reaction to his other findings. The refugees soon to arrive on Axista Four are already fleeing one war zone, and if there are hostile aliens on the planet, Cartor intends to eliminate them before the refugees arrive. Realising that he’s out of his depth, Freedom decides that there’s only one realistic course open, and at his request, the Doctor agrees to help revive Kirann Ransome to take charge.

Despite Jamie’s assurances that he means no harm, Max decides to administer a truth drug to him, resulting in such bizarre claims that Max doesn’t know what to think. He thus locks Jamie back up with Billy Joe, who is appalled by the Realists’ treatment of his friend and begins to believe that the others in town were right about them all along. Meanwhile, Lorvalan and Zenig locate the Realist base, and, assuming it to be the main human settlement, are infuriated to find that the humans built their own community in the remains of the Tyrenian settlement which they destroyed. While trying to gather information for their attack, they overhear the humans discussing Jamie’s capture and interrogation -- but, unable to hear the entire conversation, they erroneously conclude that the humans have captured Dyselt, and plan to rescue him.

On the way to the colony ship, Dee admits to the Doctor that she used to be Max Forde’s lover, but when the Realists split from the colony Max took another lover -- Hali Devine, whom Dee had always treated as a kid sister. Viewing the colony ship from the outside, the Doctor notes unusual patterns to the damage, but sets this mystery aside for later. The cryogenic security systems shut themselves down after the last failed resuscitation attempt, and the Doctor thus connects himself directly to the virtual reality systems to grant himself authorisation. As he does so, however, he is unexpectedly contacted by a future incarnation of himself, who’s been reading his diary and realised that his past self needed some help. He thus advises the Second Doctor to use a certain data crystal when the time comes. Irritated by this encounter with his meddlesome future self, the Doctor resumes his work and successfully revives Kirann Ransome, using his sonic screwdriver as a defibrillator when she goes into cardiac arrest. When Kirann wakes, she is somewhat surprised to learn that she’s been asleep for 100 years; however, she soon pulls herself together and is ready to be brought up to date.

Administrator Greene contacts his superiors on Earth and learns that the Doctor is a notorious meddler whose presence may complicate Greene’s agenda. Greene decides to question Zoe, but she has recovered and gone in search of the Doctor and Jamie. Surprised to find herself on board a spaceship, she hacks into the computer system through a shuttlecraft in the landing bay to find out what it’s doing here, and learns that Cartor understated the extent of the refugee problem; there are 80,000 new colonists on the way, and life on Axista Four is going to change beyond recognition. Cartor’s men locate Zoe in the landing bay, but she launches the shuttlecraft, determined to warn the colonists of what’s coming. As the shuttle emerges from the landing bay, Zoe sees the asteroids orbiting the planet and recognises them as defense satellites -- but Cartor, furious, then has the shuttle shut down remotely, including its life support.

Billy Joe tries to break out of the prison hut by prying open the ceiling tiles, but finds that the ceiling space is entirely self-contained. Before he can return to the cell, Lorvalan and Zenig attack the compound with robot drones, catching the Realists entirely by surprise. The Tyrenians are themselves surprised when they discover that the Realists’ “alien” prisoner is a human, but before the dissatisfied Lorvalan can kill Jamie, Billy Joe leaps out of the ceiling and surprises him. As Jamie and Billy Joe fight the Tyrenians, the Realists regroup and fight the drones, and Hali manages to reach the communications system and send out a distress signal. Cartor authorises Veena to go to the rescue, and since the shuttle which Zoe tried to steal is already ready to go, she takes that one, taking Zoe along with her. However, she’s also coming to suspect that her commander knows more than he’s saying about the alien attack.

Kirann is not impressed to learn that “Back to Basics” has become a rigid ideology; it was only ever intended as a set of guidelines to help the colonists live a simpler and more productive life without relying on technology they didn’t fully understand. When she learns of the attack on the medical centre, she reveals that it has an automatic security system which may have recorded the attack. As they set off to investigate, she greets the Doctor as an old friend, and the Doctor is irritated to learn that his future incarnation has been meddling again; not only did he introduce himself to Kirann back on Earth in order to save his past incarnation the trouble of convincing her to trust him, he’s also given her a data crystal to pass on to his past self. Unfortunately, at the moment the Doctor has nowhere to read it.

When the Doctor views the security footage from the attack, he recognises the alien attacker as a Tyrenian, one of a species of noble but nomadic warriors who appeared as if from nowhere in the previous century. Their home world was never identified -- but is it possible that they were on Axista Four first? If the planet was already inhabited, the human colony should never have been established. The Doctor and Kirann decide to return to the colony ship, suspecting that there’s more to the story of its crash than they know...

The Tyrenian battledroids prevent the Realists from getting in to help Billy Joe and Jamie, but Veena and Zoe arrive to provide support. While Veena pilots the shuttle, Zoe opens fire on the battledroids, but she underestimates the ship’s firepower and blows a hole in the side of the prison hut. Jamie has already wounded Zenig, and Lorvalan is forced to abandon him and seize the opportunity to escape while he can. As the Realists cope with the aftermath of the attack and secure Zenig, Billy Joe decides to return to Plymouth Hope, and Zoe passes on the news of the refugee problem to the Realists before accompanying Billy Joe to deliver the news to the now-recovered Kartryte. Jamie remains with the Realists, while Max, unsure whether he can trust the Federation officers, decides not to tell them about the alien bunker in the caves.

The Doctor and Kirann access a backup memory hub in the wreck of the Big Bang, and learn that some disaster struck while the colonists were preparing to shuttle down from orbit. Some files seem to have been deliberately erased, however, and when the Doctor tries to coax further information out of the computer, he finds a brief video image which implies that the ship was shot down -- which would further imply that the Tyrenians were here first after all. Intending to learn the Tyrenians’ side of the story, and noting that even the Realists use horses for transport, the Doctor rigs up a scanner to locate emissions from high-tech vehicles and uses it to trace the path of the attacker’s skimmer, presumably back to the Tyrenians’ base.

Cartor questions the hostile Zenig, fails to get any useful information out of him and demands that he be locked up without food and water. Zenig escapes when a sympathetic guard brings him food against orders, or so he believes; in fact, Cartor has secretly attached a tracer to him and allowed him to escape in order to lead the marines to the Tyrenians’ base. Max decides to take Jamie to the bunker first, hoping to avoid bloodshed, but when Hali learns that Cartor plans to launch an all-out attack on the aliens she reluctantly tells him about the bunker, fearing that Max and Jamie will be caught in the middle if Cartor goes in without knowing that they’re there. Cartor, furious with Max and Jamie for pre-empting his plans, sets off for the bunker with his men -- but Zenig is in fact heading for the Tyrenians’ ship, and Lorvalan is already at the bunker, waking the sleeping Tyrenians and preparing for war.

As the Doctor and Kirann follow the path of Kirann’s skimmer to the caves, the Doctor detects a more powerful source of energy nearby and diverts to investigate. The Tyrenian ship is hidden behind an invisible shield in a nearby lake, but the Doctor’s sonic screwdriver makes short work of the shield and once inside he reprograms the AI to believe that he’s the captain. The computer logs confirm the Doctor and Kirann’s fears; the Tyrenians were in fact here first, and the Big Bang was shot down by their automatic defence system. The human colony should never have been established here; they are the invaders, not the Tyrenians. Before they can learn more, however, Zenig arrives and captures them, and as he prepares to transmat them to the bunker, the Doctor sees too late that the Tyrenian ship contains readers he could have used to examine the data in the crystal which his future incarnation passed on to him.

Max and Jamie enter the Tyrenian bunker, but before they can learn anything they are attacked by Dyselt, whose condition has deteriorated further. Dyselt savagely mauls Max before Lorvalan arrives, but Lorvalan underestimates the extent of Dyselt’s savagery and attempts to stun him. The stun setting maddens Dyselt, who attacks Lorvalan and strikes a mortal blow as Lorvalan shoots and kills him in turn. Zenig then arrives via transmat to find Jamie standing over his commander’s dead body, and before Jamie can protest his innocence he finds himself surrounded by the Tyrenians whom Lorvalan had revived. The marines then attack the bunker, and in the confusion, the Doctor, Kirann and Jamie escape with the grievously injured Max. The marines are forced to retreat before the Tyrenians, but although both sides are now preparing for open war, the Doctor still hopes that he can negotiate a peace settlement.

Veena gives Zoe and Billy Joe a lift back to the colony, and Zoe delivers her warning about the refugees to Tam Kartryte. Kartryte seems to take the news well, and admits that, as sheriff, he has access to technology he’s never been able to bring himself to use. At his request, Zoe plugs into a virtual reality network to see the truth about the colony ship’s crash, but the neural feedback is too much for her to handle. The Doctor arrives just in time to free her from the systems, and while he tends to her, Kartryte introduces the townsfolk to Kirann -- who shocks many by revealing that they’ve misinterpreted the “Back to Basics” philosophy. They were meant to seek simple solutions to their problems without over-relying on technology, not to eschew technology completely. Even without the extra refugees on their way, the colony is overdue for change.

Zoe recovers from her experience and reveals that the battledroid which attacked her and the Doctor when they first arrived is only one of an army lying dormant in the wreck of the colony ship. In order to get Federation backing for his colony, Ransome was forced to take along an army of battledroids which could be activated remotely in case of an emergency on the frontier; apparently he intended to dispose of them upon arrival, but when the Big Bang was shot down, the battledroids responded automatically and wiped out the Tyrenian settlement, apart from those who retreated to the bunker. The Doctor claims that Ransome actually lost his life trying to bypass the ship’s AI and shut down the battledroids, but Zoe isn’t so sure.

The Doctor still hopes to negotiate peace with the Tyrenians, and he and Jamie approach the invisible ship under a white flag. However, the Tyrenians take them prisoner, refusing to let Lorvalan’s death go unanswered. Frustrated, Jamie accepts Zenig’s offer to settle the matter by ritual combat, but then learns that the fight will be to the death. He and his opponent, Gorhay, will duel with swords in an arena bound by a force field; each time someone touches the field, the voltage will increase, and the third shock will be fatal. As the fight begins, the Doctor uses his sonic screwdriver to break out of the cell -- but before interrupting the duel he uses one of the Tyrenians’ data crystal readers to find out what his future incarnation wanted to pass on to him.

Max is receiving medical treatment on the Hannibal, and the Realists and Loyalists are learning to set aside their differences and join together under Kirann’s leadership. But the colony now faces a threat from an unexpected direction, as Greene and Cartor both know the true history of the Tyrenians -- and Greene has the authority to order Cartor to commit genocide. Cartor activates the battledroid army in the Big Bang, but Veena, unwilling to be a party to genocide, takes Zoe to the Hannibal to try to talk sense into Cartor. When she arrives, however, she finds that Cartor, unable to bear the guilt of being unable to disobey orders, has slit his wrists -- after ordering the battledroids to wipe out everybody on the planet, the colonists included, so the newly-arrived refugees can start afresh. Despite the trauma which Zoe suffered last time, she’ll have to connect herself to the neural net once more in order to shut down the battledroids herself.

Jamie and Gorhay lose their swords and are stunned when they try to reach through the force field to grab the closest. As they recover, the Doctor arrives with news which he delivers to Zenig privately -- the Tyrenians are not alien at all, but human. The data crystal contains Ransome’s last confession, made as the colony ship crashed on Axista Four. The Tyrenians are in fact genetically engineered super-soldiers with canine characteristics, created by Ransome’s former colleague Gustav Tyren. When the military withdrew funding and the Federation outlawed genetic engineering, Ransome arranged for the Tyrenians to steal a ship and escape, and washed his hands of the matter. However, when he came to select a planet for his own colony, either through accident or subconscious guilt he used the same raw data with which he’d programmed the Tyrenians’ escape vessel. When the initial probes sent to Axista Four detected the Tyrenian settlement, the Federation ordered Ransome to exterminate them, and he didn’t have the courage to refuse -- and accepted the destruction of the colony vessel as his just punishment.

As Zenig tries to absorb this revelation, the reactivated battledroids attack the bunker. At the Doctor’s suggestion, the Tyrenians lure the attacking droids into the bunker and use the teleport to evacuate to their ship, but while the Doctor intended only to trap the droids in the bunker, Zenig sets explosives throughout the bunker to destroy them all. At the last moment, Zoe manages to shut down the army, but Zenig, who doesn’t want his people to know the truth of theie heritage and fears that he might one day let it slip, sends the Doctor on ahead with his people and remains in the bunker to die in the explosion.