Matthew Belfield is working in the fields of his homestead in Colorado. Inside the house his wife waves to him. He reflects on the miraculous recovery she has recently made from smallpox, thanks to a mysterious travelling healer. Suddenly, two riders approach, their horses sweating from a lengthy gallop. They are accompanied by a curious buzzing noise. They are gaunt figures in long dark coats. One, who dismounts, has an eagle feather in his hat. There is also the smell of rotting meat about them. They demand to know where the healer is, saying that he is a thief. Not liking the look of them, nor wanting to give up the man who saved his wife, Matthew denies any knowledge of the healer. The first rider, Kutter, says that this is a lie. They can see his trail. Kutter produces a huge gun from his holster and points it at Matthew. Behind him, Matthew hears his wife Celeste cocking their shotgun. The second rider, Tangleleg, says that he can see and hear the lie in their faces and voices. As he moves again Kutter is blasted off his feet by the shotgun but picks himself back up again. The two riders open fire with their weapons, sending blue rays at the house and the couple, turning everything to fire and ashes.

The two riders consult the maps in their heads and converse in the buzzing noise. Kutter gets fresh horses from the stables while Tangleleg kills their old mounts. The riders feast on raw meat and head off westwards.

Martha and the Doctor are on a Planet called Hollywood, created after NeoCalifornia was destroyed by a super-volcano in the 25th century. The Doctor has brought her here to visit the best cinema ever, but when they arrive it is closed after a floor collapsed during a showing of ‘Earthquake”. Martha is upset; she wanted to watch a western to remind her of Sunday afternoons with her family. To cheer her up the Doctor takes her back to the TARDIS and sets the controls for the real Wild West.

They arrive in a western town, just after breakfast on a Monday morning in the 1880s (according to the Doctor’s nose). The town is partly finished: there are tents and half-built houses. There are also four bodies in pine caskets outside the undertaker’s premises.

The schoolteacher, Jenny Forrest, is making her way down the street with some books she has inherited from the recently deceased Toomey. She discusses this with Sheriff Blaine, who remarks that it is a blessing that so few died, though Jenny is more doubtful about the nature of this blessing. He invites her to the street party being held that evening to celebrate the survival of so many townsfolk. She replies that she may come if she has the time. Moving on down the street she sees the Doctor and Martha ahead of her and by their voices and clothes decides that they are from the East. She is puzzled because the stagecoach from Dekkerville isn't due for a week but they imply that they have ridden into town on their own ‘transport’. Martha is alarmed to hear that there has been an outbreak of smallpox; by rights the town should be in the grip of an epidemic that could wipe out most of the people. Jenny tells of how a travelling medicine showman called Alvin Godlove arrived at the start of the outbreak and cured the sick with a remedy from a bottle. Even she, who doubted the efficacy of such things, bought one. The Doctor takes the bottle to the TARDIS to investigate it further but only discovers alcohol, rock salt, sugar and a hint of chocolate.

While he is gone Jenny is instructing Martha on the founding of the town of Redwater. She also suggests that Martha’s clothes are less conservative than the prevailing fashion. They encounter Zachariah Hawkes, editor of the Redwater Chronicle. He practically ignores Martha, and when she asks to see his newspaper (he is carrying a bundle of them) he is dismissive of her ability to read. That is, until she points out a number of spelling mistakes.

The two women carry on their walk, noting how there is an air of forced jollity about the town, as if the townsfolk fear to doubt the miraculous nature of their survival. They are interrupted by Joseph Pitt, owner of the livery stable, who tells Jenny that there has been a break in at the school. When the three get there they see a window has been broken and inside there is a young man, Nathan, inside. He says he has gone there to escape the visions in his head, scenes of metal men, things like lizards and birds, guns that shoot lightning and clouds in the shape of mushrooms. To Martha these dreams sound like a nuclear war involving robots and aliens, but before she can ask more Pitt drags Nathan off to demand recompense from his father. Jenny says that a number of Godlove’s patients suffer from similar visions.

The Doctor has left the TARDIS and entered a saloon. He orders a sarsaparilla. When he searches in his pocket to find some money he pulls out his sonic screwdriver. This attracts the attention of Loomis Teague who snatches the device but pays for the drink. He says that the Doctor can have the screwdriver back if he wins it at cards. They join a game at the card table. Obviously thinking he is an easy mark, the card players are annoyed when the Doctor wins back the screwdriver and then all their chips. He punctuates his victories with questions, particularly about Godlove. He finds that Godlove and his Pawnee sidekick, Walking Crow, would enter the houses of smallpox victims without fear and give them the patent medicine. Within a day they would be cured.

When the Doctor wins the final hand Teague accuses him of hiding cards in his pockets. The sheriff is in the bar and comes over to investigate. He pulls a wallet out of one of the Doctor’s pockets: it is psychic paper and says that the Doctor is a Pinkerton agent. Far from mollifying him, the sheriff threatens to run the Doctor and Martha out of town unless they desist with their questions.

Inside the TARDIS, as evening falls, the Doctor is puzzled and fascinated by the lack of clues he can discover. He tells Martha that there are no telepathic wave forms that would explain “Small community, unfriendly natives, weird happenings” and usually lead to “an alien thingy buried under a church”. They are formulating a plan of action when Jenny knocks on the door. Not wanting to expose her to the mysteries of the TARDIS they let her leave and then follow her down the street. She hears the TARDIS door close and is surprised that two of them were together in such a small shack. She has been listening to a lot of talk about them in the town, not least that they did not ride in on horses. Despite all this she finds them trustworthy and there is something reassuring about the TARDIS itself.

When they catch up with her they find that she came to Martha because of her worries about Nathan. They find out that he was one of the first to receive the cure and surmise that he may have had the longest incubation period, hence his dreams are worse. They resolve to speak to him. Nathan’s mother is long dead and his father is at the street party, having padlocked Nathan inside the house.

The sonic screwdriver makes short work of the lock and the Doctor is soon inside with Marta and Jenny. They are aghast at the walls full of racks of weapons. Nathan is less than responsive when the Doctor tries to question him about the dreams. He sings a Venusian lullaby to hypnotise the boy and then gets him to describe the dreams of aliens and robots at war. As he tells of his visions the Doctor detects a slight energy trace and Martha also notices there are no lesions in Nathan’s skin as if he has been regenerated rather than cured.

They become aware that Nathan’s father has entered the room and are shocked to find that he is Sheriff Blaine. He is angry at what he finds and seems quite threatening until they tell him they are helping his son and he becomes more defensive and fearful. At that moment they hear gunfire and see brilliant flashes of white. They race to the main street and find that Kutter and Tangleleg have entered town and killed Fess Logan. The sheriff recognizes the killers as two outlaws who died in a roadhouse fire, and like the majority of men at the scene he draws his gun. The killers demand to know what became of the healer but the townspeople answer with a volley of bullets. The outlaws move at fantastic speeds to dodge most of the bullets and even when hit do no more than spin around. Tangleleg kicks out at a few men sending them flying through the air. Kutter brings all this to a halt by putting his pistol to Nathan’s head. They say they will spare the boy if the sheriff tells them where Godlove went. He finally answers: Dekkerville. His reward is to be shot down in cold blood, and then the outlaws begin firing their energy weapons into the buildings, starting fires.

The Doctor asks them why they executed him. After noting that the Doctor is ‘unlike’ Kutter tells him that the sheriff would have gone after them and that examples have to be made. He then shoots at Nathan but Jenny pushes the boy away and takes the blast instead. Martha and the Doctor pick her up and carry her back to the TARDIS where Martha’s medical skills and some nano-technology from the TARDIS medical kit save her. They then begin to puzzle over where two outlaws in the Wild West would get energy weapons. The Doctor wants to go to Dekkerville in the TARDIS to question Godlove but Martha thinks it could draw too much attention. The Doctor agrees; if Kutter could sense the Doctor’s difference he might spot alien technology on the move. Jenny has recovered enough to overhear this and tell them that the sheriff lied and that Godlove didn’t go to Dekkerville but north to Ironhill.

When Jenny wakes again she is in her own bed. She has vague memories of the interior of the TARDIS but cannot think where in Redwater she was.

A meeting of the townspeople is called in one of the few surviving premises. The Doctor assumes control, prompting some to demand he takes over as sheriff. However, he declines and suggests the gambler Loomis Teague as the ideal candidate. Teague’s first duty is to provide Martha and the Doctor with some horses to get them to Ironhill and a guide who can show them a pass that will take a day off their journey time. As they are being equipped for the journey the Doctor accepts a hat and a holster (for his screwdriver).

Their guide turns out to be Nathan.

In Ironhill Alvin Godlove is reflecting on his days as a conman selling quack remedies. Nowadays he is using a genuine cure-all. Everywhere he goes he finds the people thrusting money at Walking Crow, who follows everywhere behind him. He has to implore the people to give him time because he has so many people to visit and cure. At the home of Mrs. Weems he is taken to the old lady’s bedroom where she is apparently breathing her last. He produces an object in the shape of a handgun. Tiny needles in the handle nip into the palm of his hand and the organic metal of the device seems to merge into his flesh. He aims at her body and an emerald light washes over her, causing the scars and pock-marks on her skin begin to fade. .

Later, Godlove is on the back stoop, sweating. Walking Crow finds him and warns him that the cure-all is taking control. Godlove tries to put him off, saying that they are richer than they have ever been, but secretly his hand is writhing with tiny wires and whorls implanted in the flesh, and a pain that is reaching into his arm and shoulder.

Nathan leads the Doctor and Martha through barren and hostile lands until they arrive at the foothills. He takes them through narrow and winding canyons until they emerge above a small town. Martha begins to enjoy riding her horse which she has maliciously nicknamed ‘Rose’. When they arrive they find Ironhill superficially similar to Redwater, but whereas the town they have left was in a mood of celebration this place is gripped by fear and disease. Houses are boarded up and there is a scent of death and decay. The stableman is taken aback by the Doctor’s energy and enthusiasm and suspects that he has come to sell something, but when he hears that they are acquaintances of the healer his attitude softens and he directs them to the widow Weems’s place. He also points out Godlove’s wagon.

In the saloon Godlove is intimately entwined with a bar girl. Three brothers, roughnecks all, are offering to do any service to repay Godlove for his work. When Walking Crow enters and tells him of the arrival of strangers and their quest for the healer, and names one as the son of the sheriff of Redwater, Godlove is taken aback. Walking Crow says it is the Doctor who worries him most, not least for his authoritative bearing. Godlove suspects he may be a United States Marshall and arranges to meet Walking Crow at their hiding place after nightfall and then asks the three brothers to take care of the Doctor for him.

Martha and Nathan make for the covered wagon and Martha slips inside. She finds two strongboxes, one full of money and the other locked but far lighter. Something rattles inside. Before she can investigate further, Walking Crow steps in holding Nathan at knife point. Far from threatening them he drops the knife and says that he knew no good would come from the cure-all.

Outside the saloon the Doctor is confronted by the Lyle Brothers who call on him to draw his weapon. At first he tries to persuade them to let him see Godlove but they threaten to kill him so he agrees to duel with them. As Godlove rides off from the town he hears the brothers’ guns but what he cannot see is the Doctor drawing his sonic screwdriver and using it to create a wall of sound that stops the brothers’ bullets in mid air before changing the setting to shiver their pistols to pieces. As the three Lyles flee the scene Martha, Nathan and Walking Crow race up to the Doctor. The Doctor introduces himself to the Pawnee as Rides in Night. Walking Crow is astonished, thinking that the Doctor has emerged from myth and legend. The Doctor asks for Walking Crow’s help to prevent the darkness that is extending over the land. He suggests that Godlove is the cause of it.

The Doctor uses his screwdriver to open the locked trunk in the covered wagon and finds fragments of metallic material which suggest the hull of some intergalactic craft. Walking Crow tells the story of where the fragments came from. He says that the healer and he were at their lowest ebb: short on money, food and water; their horse injured (and Godlove suffering two broken fingers) in an accident. From the east they saw white droplets scream overhead and fall several miles away. In the morning they tracked down a crater where the droplets fell. The strange metal was scattered around but in the crater was a small wrecked vessel, oozing thick oil. At its centre was a gun. Snatching it up, Godlove was felled with agony until a warm emerald glow emanated from the gun, healing his broken fingers instantly. Back at the wagon he healed their injured horse in the same way. That was how Godlove became a healer.

Hearing this story makes the Doctor sure that he knows in the back of his mind where the gun came from (and, with the thought of Kutter and Tangleleg, who wants it back). He performs a quick chemical analysis using ingredients from Godlove’s wagon and declares himself certain of who he is dealing with. Darkly, he adds that the news is not good.

The people of the town are not pleased that the Doctor apparently drove the healer away. Before anything comes of it, however, Tangleleg and Kutter ride into town dragging men behind their horses on ropes. As they cut them free Martha steps forward, refusing to stand by and watch more people hurt or killed. The longriders are puzzled at how she arrived in town before them. She asks why they want the healer but they say they will destroy the town in a punitive strike if he cannot be found. As they converse in their strange buzzing sound Martha recognizes it as a sound she knows, a computer sending information on a phone line. Tangleleg scans Martha and Nathan with an orange light from his gun and sees that the boy has been marked and then fires a bolt of energy into the feed store, setting it ablaze. The Doctor steps forward and invokes the 15th Proclamation of the Shadow Convention to instigate parlay. The riders accept.

They recognize the Doctor as the last of the Time Lords and he recognizes them as Clades: intelligent weapons that turned on their humanoid masters and wiped out an entire civilization millennia earlier, their sole reason for existence is war. Power and wealth do not impress the Clades; they only seek to destroy things. Once invented as Peacemakers, ultimate weapons that terrified anyone into harmony lest they be used, now they operate as mercenaries. Walking Crow recognizes that the corpses of Kutter and Tangleleg are not the Clades, merely the hosts: the Clades are the guns that the outlaws are carrying.

The Doctor surmises that these two Clades have been sent to recover a command unit that crashed to Earth. When Godlove found it damaged it was self repairing and he could use its regenerative capacity as a cure. Once it has healed itself it will seek war. The dreams and visions it is leaving in those that it cures are actually battle reports from its activities in a million conflicts from across the galaxy. Walking Crow, overcome by the guilt that he had a part in such events, tells Martha where Godlove has gone to hide outside the town.

The healer is in an old iron mine cavern. He tries to put the Clade gun down but it will not let him. Cables and cords emerge from it and pierce his flesh and bone, boring through him until the weapon is part of his body and in control. What used to be Godlove is a prisoner in his own mind, screaming.

The Doctor tells the Clades that they cannot eat him because they have no imagination outside the battlefield but they respond by shooting Martha. As she loses consciousness she tells the Doctor where Godlove is hiding. As Walking Crow tends to her wounds the doctor confronts the Clades. They inform him that they used a low energy beam to create a degenerative wound. She will die slowly unless she is treated by Godlove’s cure-all. The Doctor has to take them to Godlove to save her. He agrees.

The Doctor, Nathan and Walking Crow put Martha in the covered wagon and set off for the mine, followed by the two Clades on horses. As they near the mine the Pawnee accelerates the wagon on a long slope to get clear of the riders, then brakes sharply, swerving to block the narrow pass. He tells the Doctor to get Martha to the mine with Nathan’s help. As they do so the riders set fire to the wagon blocking their way. Wounded Crow shoots an arrow into Tangleleg’s eye, only to see his victim snap it off before returning fire and killing him. By now the other three are in the mine and the Doctor uses his screwdriver to release a rock fall that blocks the entrance to the mine, unfortunately burying himself in the process. Martha gives Nathan her mobile phone to give them some light from its screen and then, somewhat dusty, the Doctor emerges from the rubble.

The two Clades outside the mine survey the rubble and assess that blasting it will only cause larger rock falls. Instead they survey the scene and spot a ventilation chimney higher up the hill. Inside the mine the other three make their way to their confrontation with Godlove. When they find him he looks as f his body is decaying and he speaks as if he was already a Clade, although he retains some of the speech patterns and vocabulary characteristic of his former self. Attached to his hand by festoons of wire is the gun, now grown to enormous proportions. He says he enjoys the way that Godlove expresses himself and it seems as if the Clade has adopted a great deal of its hosts personality in the time that it was regenerating itself from the crash.

When the Clade refuses to heal Martha, because it sees no value to itself in the action, Nathan rushes forward and pushes a pistol to its head. The Doctor appeals to Nathan not to kill, saying it would make him no better than the alien. Nathan relents and drops the gun. The Doctor asks for Martha to be spared in return for his saving of the Clade’s life. The alien says that firstly he and the Doctor are going to make a deal.

As Kutter climbs down the ventilation shaft he falls and breaks his leg. Healing himself with his gun he notes that the process is taking too long. When Tangleleg joins him they agree that their host bodies are failing them and that finding new ones will be problematic. Their combat functions and memory banks are already clogged by the residual memories of the forms that they inhabit. Disturbing a rattlesnake causes Tangleleg to be bitten but he is confident that his systems will deal with the toxins, possibly replicating them for future use. He attaches fine wires from his gun to the snake’s head and probes for recent memories - this technique only works on lower order creatures - and finds that humanoids passed by recently. He rips the snake in two and they feast in silence.

The Clade in Godlove’s body is suffering similar problems; the healer’s body is crumbling. He demands that the Doctor gives up his more resilient body in exchange for Martha’s life.

When the Doctor agrees and takes hold of the gun there is a transfer of energy and power that leaves Godlove dead on the floor and the Doctor with the wires penetrating his own body right down to the internal organs. He fights the effect long enough to use the weapon to heal Martha, including the hole in her jacket from the shot that injured her. She goes to the Doctor who is trying to master the Clade’s influence. She is aggrieved that he should sacrifice himself for her. When the Clade speaks it does so in Godlove’s voice, saying that it can overcome the Time Lord’s will but the Doctor regains control long enough to tell Nathan and Martha to run away.

As his friends flee down the tunnel the Doctor enters into an internal conflict with the Clade. It shows him the bodies of his friends and companions: Sarah Jane, Mickey, Rose, Martha, Captain Jack and K-9. They are all engulfed in the horrors of war. It taunts him with his deeds in the Time War, visions of the millions of battle TARDISes and Dalek saucers and it offers him the chance to join with the Clade and eradicate the Daleks forever, along with every other menace in the Universe. It says that the Cybermen would be dead and Rose still with him if only he had been a Clade.

Further up the tunnel Martha comes to her senses and realizes that she cannot abandon the Doctor. She turns back and Nathan, despite his doubts, turns with her. They find the Doctor as he is struggling weakly within himself, looking for the command protocols that originally controlled the Clade, the orders that they broke before they became remorseless killers of their own masters. He tells Martha it is too dark within him to fight on so she offers him some sparks and kisses him. This restores his purpose. It gives him the strength to repair the broken command data chain (and make some more alterations), as well as reject the cables infesting his body.

He is sitting, staring into space as if oblivious to his surroundings, when Tangleleg and Kutter arrive in the cave. They note that the weapon they are seeking has a new host but remark that this is not a mandated action, that recovery is paramount. A small saw emerges from Kutter’s gun and he steps forward to sever the Doctor’s arm. The Clade reveals the plan: take back the lost weapon and depart for the intended warzone, using nuclear warheads to destroy the landing site as they go. The Doctor snaps back to consciousness and smiles at Martha. He steps up to the Clades and offers them the weapon in return for their departure. They agree but say the zone will still be sanitized. The Doctor then tosses the gun towards an open elevator shaft in the centre of the cave. Both Clades reach to grab it and as their hands grasp the gun it spits out wires and cables that penetrate their skin. As the two stand transfixed the Doctor tells his friends to run. Martha detects ultrasound shaking the tunnels and caverns as she escapes. Behind her the three Clades are trapped in a spiral of negative commands, overloading dangerously, only able to utter the forlorn curse, “Doc-tor!”

Martha and Nathan emerge from the ventilation shaft into the sunlight as the first tremors of an earthquake strike the hill. The Doctor appears and races down the slope to them as the hill collapses in on itself, crushing the host bodies and the Clade weapons, destroying them completely. One final telepathic signal escapes, appearing above the mine as an emerald bubble that expands across the countryside. After it has passed Nathan says that the fear and apprehension associated with the nightmare visions has gone. The Doctor admits that he caused this to happen while he was in the Clade program matrix. After burying Walking Crow they return to Ironhill for a bath and a night’s sleep at the hotel. The Doctor spends his night on the balcony, watching stars all night.

In Redwater, Jenny Forrest promises to look after Nathan. It is apparent that she has become considerably more friendly with Loomis Teague. She follows the travellers to the TARDIS with Nathan. He remarks that he expects it to sprout wheels and roll away once the Doctor and Martha are inside. Instead, the door opens and the Doctor re-emerges with a copy of H.G. Wells “Time Machine” for Jenny, saying that it will explain a lot. She notes that its publication date is ten years in the future but he just asks her not to lend it to anybody apart from Nathan.