The TARDIS materialises on a forgotten world in the depths of space. The Doctor emerges, annoyed that his ship has either malfunctioned or chosen to bring him somewhere uninteresting. He is located near some empty buildings, corroded and dusty. He finds a monitor screen and uses the screwdriver to get access to the system. He is in Lodestar Station 479, a disused refuelling station. Then he notices that the computer’s sub-routines have been tampered with and decides to search out the data core. He enters the building nearest to him, it smells like an old refinery, and finds a corridor and a sign that tells him where the core is. Arriving at the door he needs the screwdriver to enter. Inside is the desiccated skeleton of a human. Before he can solve this puzzle the door closes behind him. He tries the screwdriver but this time it is ineffective. He is trapped.

The Wayfarer is a converted naval patrol vessel, rescued from the scrap yards twenty years earlier. It is home to Jon Bowman, the captain, and his crew. Currently the ship is damaged after a skirmish with pirates and needs to make repairs and refuel. They are right on the edge of Earth space and the only possible salvation is a former frontier post called Hurala.

They land near some old buildings and leave the ship to explore. The crew consists of Bowman, Stella, Scrum (the computer expert) and Cuttin’ Edge (a young ex-marine).They move towards the buildings, followed at a distance by Koral, the fifth member of the crew. She is a tall, humanoid alien who seems to act as Bowman’s bodyguard. A shout from Cuttin’ Edge takes them over to the TARDIS. They are puzzled by the fact that it is humming and the lights are on but their repairs and refuelling are the priority so they move on. Scrum is using a scanner and reports an unusual signal deep underground. He is astonished when he realises it is an SOS signal.

Eventually they trace the signal to a door at the end of a long underground corridor. When they open the door they are greeted cheerfully by the Doctor. They immediately distrust him and search him. Stella in particular finds it hard to believe his claim that he has been there for five days. The captain orders the crew to start refuelling the ship. Scrum says he, too, has noticed an unusual signal in the computers but Bowman is not interested and sends Scrum back to fuel the ship. Stella wants to know who locked the Doctor up and why. The Doctor decides to investigate the computers and finds that the new signal is an override system intended to trap visitors in the room. He suspects that the corpse is the remains of one of the installers of this system who suddenly became expendable. He has also found that once the trap has been sprung a signal is sent but he can’t find out who it is sent to. Before an answer can be found the door leading into the corridor explodes open and three Daleks stare at them, shouting “Exterminate!”

As the first Dalek opens fire Cuttin’ Edge blasts it with automatic rifle bullets, enough to distract it while the humans escape up the stairs. His second attempt is a single bullet that causes a burning dent in the Dalek, a molecular dissolution virus. As they run the Doctor asks how the bullet was so effective and he is told that the Wayfarer crew are Dalek bounty hunters. Dodging and weaving through the complex the Doctor tries to lead the humans to the TARDIS but they are cut off by other Daleks and have to race to the Wayfarer. Scrum has the engines running and Koral is already aboard as the others run up the ramp. An explosion hits the ship as they lift off, injuring Stella. As the Doctor tries to help her the interior air lock door buckles and a Dalek exterminates Stella. Cuttin Edge shoots at it while the Doctor flings a cryogenic charge that he had intended to use on Stella at the Dalek, immobilizing it instantly. Bowman orders them to throw the Dalek off the ship but the airlock door is too badly damaged. The Doctor blames himself for not acting quickly enough to save Stella and the crewmembers are in agreement saying that their troubles began when they found him in the prison.

The Doctor examines the defunct Dalek while Cuttin’ Edge works nearby on the airlock. They talk about the molecular dissolution virus that Scrum invented. Cuttin’ Edge can’t understand why it was so effective on the planet but hasn’t damaged the Dalek on the ship. The Doctor tells him that the first damaged Dalek would have analysed the threat and transmitted new defensive protocols to other Daleks in the area. Cuttin’ Edge begins to tell the Doctor about their operation; they are employed as bounty hunters by Earth Command, getting paid for every eyestalk that they collect. The Doctor is perplexed by his own arrival at this point in history, before the Time War even started. This should be impossible but somehow he is in the middle of the first Earth Empire’s war with the Daleks. Cuttin’ Edge says that the war is finely balanced and that he is part of the generation that has never known a time when the war wasn’t in progress. He says he was discharged from the marines for being too much of a loose cannon and joined up with Bowman, a veteran of the Draconian Conflicts. Their conversation is interrupted by Scrum, informing them that they are taking Stella’s body back to her home on Auros.

Later in the voyage Scrum suggests taking the Dalek apart to see what can be learned from it. The Doctor warns him about all the defence systems. The Doctor makes his way to the engine room to see if he can improve their performance but is pounced on by Koral who tells him that Bowman wants to see him. In the captain’s quarters Bowman questions the Doctor about his presence on Hurala, and why the Daleks were there, too. Before the Doctor can answer they arrive in orbit around Auros, where something is terribly wrong.

The whole planet is on fire while fleet of ships evacuates. The Doctor recognises the Osterhagen Principle in action: the thousands of colonists have boarded an escape fleet and detonated nuclear devices beneath the surface to render the planet unusable for the Daleks. The Doctor is appalled that humans could do such a thing but Bowman says the planet is too far from Earth Command to be defensible. Suddenly the Doctor turns his thoughts to the events unfolding in front of him and becomes horrified for another reason. He demands that the fleet is sent a signal warning them to turn back but even as he makes contact his transmission is blocked by the Daleks. They demand that the fleet surrender. When the Leader of the fleet begs for safe passage her ship is destroyed and the rest of the fleet is taken prisoner.

Bowman wonders how the Doctor knew this would happen but the Doctor puts it down to guesswork. Bowman attacks the Doctor as if blaming him for these events, saying that the Doctor knows more than he is telling. The Doctor says that if it makes them feel better they can beat him up but Koral steps in and points out that they should be fighting the Daleks and not each other.

Bowman and Scrum decide to see if their captive Dalek can answer their questions. They all go to the cargo chamber where the Dalek is stored. It is beginning to thaw out. Using a stethoscope the Doctor discovers that the creature is still alive. Scrum suggests that they open it up and ask it some questions. The Doctor asks why they don’t take it back to Earth command but Bowman says it is too far. When the Doctor says that Bowman doesn’t understand the Daleks he is contradicted by the captain. Bowman says that he know that Daleks deliberately reduce the power of their weapons so that it takes a few seconds to kill humans, making sure that they die in agony. The Doctor says that he knows that but he still thinks they want revenge for Stella’s death. Bowman merely agrees.

Cuttin’ Edge uses a cargo loader to turn the Dalek upside down and then prepares to open it up. Despite his objections the Doctor helps them to remove the Dalek’s gun. He says it is because he doesn’t want anyone else to get hurt. When they prepare lasers to cut the casing the Doctor objects again, telling them that they are committing murder. Koral then steps in and produces razor-like claws from her fingers. With precision and strength she opens the casing up to reveal the creature inside. Scrum and Cuttin’ Edge use staves to remove the creature from the casing but it catches inside and hangs, suspended. Its eye opens.

When the Dalek refuses to speak in response to Bowman’s questions he orders his crew to use torture. The Doctor tries to stop them but the three men threaten to kill him. Powerless, the Doctor leaves. He determines to gain access to the ship’s systems to stop them but Koral finds him and says she has been sent to stop him doing anything silly. A scream is heard from the cargo bay as the torture begins. The Doctor tries to go back but Koral tells him on her home planet, Red Sky Lost, her people used their claws to hunt and kill koogah beasts. The Doctor asks if they tortured the beasts first but Koral does not reply. Instead she tells him that the Daleks destroyed her planet and she is the last of her people. The Doctor tells her that he understands. More screaming follows. The Doctor tells her he can get information from the Dalek. Just then Bowman emerges, announcing that the Dalek is dead and that it never said a word. Scrum and Cuttin’ edge follow him, their faces etched with distaste at what they have done.

The Doctor enters the cargo bay. The remains of the Dalek lie on the floor. As the Doctor crouches beside it he eye twitches. The Doctor whispers to the Dalek, telling it that he is the Oncoming Storm. The Dalek calls him “Doctor” in return. They converse briefly, during which the Dalek lets slip that the Humans can never win the war and that the Daleks will be the masters of Time and Space. As the Dalek dies the Doctor suddenly realises why they were on Hurala and rushes away, leaving Koral in the shadows, unseen.

The Doctor finds the three men in the galley and asks what they know of the Arkheon Threshold. He tells them of his conversation with the Dalek but they don’t believe him until Koral confirms the truth. The Doctor tells them that the Daleks must have been on Hurala looking for information about the planet Arkheon. Scrum tells him that the planet was destroyed forty years earlier but the Doctor says that it doesn’t matter; the Threshold will still be there.

He tells them that Arkheon was known as the Planet of Ghosts due to temporal anomaly creating spectral visions. Deep inside the planet was a chronic schism, a small tear in time and space called the Arkheon Threshold. The Daleks could use it to control Time and wipe humanity from history. The crew reluctantly comes to agree with the Doctor’s speculations and allow him to pilot them to the Arkheon system. In order to get there quicker he tunes up the Wayfarer’s engines. When they get there they find only half of a planet with its molten core exposed to space. Scrum reports that there are no other space ships in the vicinity as they come in to land. They pass over a snowy landscape of ruined cities and land near the outskirts of a former metropolis.

They make their way through the frozen landscape, gradually becoming aware of movement around them. The Doctor leads them on towards the source of chronon activity. Suddenly, he is thrown to the floor by a humanoid shape in a shroud. Bowman and Cuttin’ Edge kill it instantly. The Doctor inspects the corpse and declares it to be a devolved native of the planet, reduced to scavenging. Bowman says it won’t be alone. Instantly, a pack of the creatures attack forcing the Doctor and the Wayfarer crew up into the rocks. As they reach the top of the crags they realise that they have reached the edge of the world and are looking down a cliff that falls to the molten centre of the world. The Doctor’s excitement at the spectacular view is barely tempered by the closing forces of their new enemy until a sudden thought hits him. Before he has time to apologise, a party of Daleks rise up in front of them, exclaiming that the crew are now all prisoners of the Daleks.

They are herded onto a platform that descends to the mouth of an enormous caver and then moves inside. The cavern is full of criss-crossing walkways and landing areas. Hundreds of Daleks are going about their business. The Doctor is full of self recrimination; he realises that the Daleks must have been there for years in order to create something so vast. Bowman says that there have been rumours of a secret Dalek base where prisoners are taken to be interrogated and experimented on. Its nickname is ‘the Black Hole’ because nothing ever came back out. The prisoners are scanned for their ability to work in the mines. As Bowman is scanned the Daleks detect that he has had a subcutaneous transmitter removed, revealing him to be a high ranking Earth Command officer. A brain scan tells them that he is Space Major John Bowman and they order him to be taken for interrogation. Koral tries to attack the Daleks but is pulled away. In punishment the Dalek’s kill the weakest member of the party: Scrum. Cuttin’ Edge tries to stop them but the Daleks paralyse his legs.

Cuttin’ Edge tries to force the Daleks to kill him but they pick him up and order him to report to the mines. As Bowman is being led away Koral pleads with the Doctor to intervene. The Doctor asks the Daleks if they know who he is. He whispers to the nearest Dalek and it scans him, recognising him immediately. Agitation spreads through the Daleks in the cavern which impresses Cuttin’ Edge. The Doctor is marched away to a security room and scanned again. The Command Dalek tells the Doctor that the Dalek Inquisitor General has been ordered to attend the Doctor’s interrogation.

The mines are incredibly hot. Survivors from the Auros fleet are being forced to labour in teams of four. There is an hourly audit by the Dalek supervisors, after which the weakest labour team is exterminated. Despite being barely able to stand, Cuttin’ Edge knows he must work hard to prevent his team (Koral, a woman and her twelve year old daughter) being next to die.

In a cell deep inside the complex, Bowman and the Doctor discuss their situation. The Doctor surmises that they have been caught in a trap. The Dalek they tortured on the Wayfarer used its last moments to hint at the Arkheon Threshold to fool the crew into going there. Bowman confesses that he was less than enamored when he was given a desk job by Earth Command so he cut out his chip and went on the run, setting himself up as a Dalek hunter. The problem is that the Daleks know the Earth defence system is wired into his brain. The Doctor asks if he has heard of the Dalek Inquisitor General and Bowman replies that it is known as Dalek X (his Space Service security designation), the most feared Dalek in the war.

Even the Inquisitor has adopted the name Dalek X because of the fear it inspires in humans. His sole purpose is the extermination of the human race and his only superior is the Supreme Dalek on Skaro. He rides into the Arkheon system aboard an Exterminator class warship, the first of its kind and the ultimate Dalek space craft, armed to the teeth and containing five hundred crew members. Its purpose in coming from Skaro is to interrogate the Dalek’s definitive enemy, the Doctor. Dalek X is black and gold, as opposed to the bronze of the other Daleks. Arriving at the base on Arkheon, Dalek X is less than pleased at the mining operation running behind schedule and orders the mine leader Dalek exterminated. He orders the humans in the mine to be made to work faster.

The Doctor and Bowman are moved out of their cell: Bowman to have his brain removed and the Doctor to be interrogated. The Doctor is led into a dark room and secured against a wall by metal bands around his ankles, wrists and head. Dalek X explains that it is a mind probe machine. Power runs through the machine and into the Doctor, causing him great physical pain. Through a foggy mind the Doctor starts to put a pattern together of why the Daleks slaughtered the Auros fleet and why they are so determined to break through the Arkheon Threshold. He realises that the Daleks are in danger of losing the war. Dalek X says that defeat will not happen because they are going to change history. The Doctor says that there isn’t enough power to do this but Dalek X taunts him by showing him the molten core of Arkheon and saying that there is a way through it into the Time Vortex; they will use it to gain mastery of Time and Space.

Before Bowman is opened up he is shown a view screen of the Wayfarer being destroyed on the planet’s surface

The Doctor is taken on a guided tour of the cavern, ending at a massive machine (five storeys high): the large chronon collider that will break open the Threshold. The Doctor agrees that it might work but says it will need to be stabilised, and only a TARDIS could do that. When Dalek X suggests the Doctor’s TARDIS, the Doctor refuses point blank. No form of coercion seems likely to work until Koral, Cuttin’ Edge and their two workmates, Jenifa and her daughter Kuli, are brought before him. As the Daleks prepare to exterminate them, the Doctor consents to let them have his TARDIS. However, he adds that the TARDIS needs a crew of six people. He demands the four in front of him and Major Bowman. Dalek X tells him he cannot take the mother and daughter; he will have to make do with a crew of four.

As Bowman is summoned the Doctor tells the Daleks that his TARDIS is disabled with a broken spatial motivator. He says it will do what the Daleks need it for but the time rotor needs to be removed.

The Doctor and the three Wayfarer survivors are taken aboard the Dalek flag ship, Exterminator, and within the hour are back on Hurala. Soon, they are standing outside the TARDIS with a party of Daleks. The Doctor pretends that he has lost the TARDIS key and says he probably dropped it when he was trapped in the underground cell after he first arrived on the planet. Dalek X, some elite guards, the Command Dalek and a group of assault Daleks lead the Doctor and his companions down a flight of stairs towards the cell. Cuttin’ Edge uses the narrowness of the stairs to his advantage. He wraps a chain round one of the Daleks and tips some machinery that the chain is fastened to down a stair well. The Dalek plummets, colliding with others. In the confusion the Doctor, Bowman and Koral make their escape into some service hatches, but Cuttin’ Edge is exterminated.

The Doctor leads the two bounty hunters to the astronic fuel silos. He tells them that the return to Hurala was just a ruse to achieve this objective and that the fuel residue ion the silos is enough to destroy the Exterminator. While Bowman holds off the Daleks by using the confined space, and by employing various pieces of heavy machinery as weapons, the Doctor improvises a huge bomb. Dalek X, arrogant in its belief that it can resolve this situation alone, tracks the Doctor down. Koral has been lying in wait and ambushes Dalek X from beneath, holding it still long enough for Bowman to fire a succession ion bolts into the casing. He then tips the blazing Dalek into the darkness of a huge silo.

The Doctor finishers his bomb but realises it will have to be detonated manually. Bowman volunteers to stay behind, saying he always felt that this was a suicide mission. Koral is horrified and declares her love for Bowman. Bowman replies that he loves her, too, which is why he wants her to escape. He then uses a nerve grip to knock her out. The Doctor carries Koral back up through the complex and into the Hurala night. They sprint to the TARDIS and make it inside before the Dalek guards are aware of them.

A party of Daleks closes in on Bowman just as he pulls the lever, starting a chain reaction in the fuel silo beneath the ground. As the Daleks flee Bowman prepares to die. Instead he sees the TARDIS materialise in front of him and Koral reaching out to pull him inside. As the TARDIS dematerializes again the fuelling station and the town around it are vapourised. The fleets of Dalek ships, including the Exterminator, are destroyed in the blast.

The Doctor takes Bowman and Koral to Earth where they report on the events leading up to the destruction of the Dalek fleet. Afterwards Bowman tells the Doctor that he is giving up active service and intends to take Koral to meet his parents.