Tegan is travelling with the Doctor once more, but this time it’s by choice, as she’s found her ordinary life on Earth to be dull and unfulfilling after her travels through time. The morning after her return, while the Doctor is checking over the TARDIS console to ensure the Time Lords didn’t install any unwanted “extras” during his visit to Gallifrey, the telepathic circuits short out; at the same time, Nyssa wakes from a terrible nightmare of Traken’s dissolution and is touched by something lurking in the darkness of her room. Fearing that something has tried to invade the TARDIS using Nyssa’s mind as a gateway, the Doctor tries to locate the source of the telepathic signal, but is knocked unconscious by a powerful psychic blast.
The TARDIS materialises on a moon with a breathable atmosphere, orbiting a world the colour of rotting blood right on the edge of the intergalactic void. The Doctor and his friends emerge from the TARDIS to search for the evil that attacked them in the Time Vortex, but the ground explodes beneath them, dropping them into the mines beneath the surface. Nyssa is concussed, but the people who set the charges get the Doctor and his friends to safety before the tunnels collapse any further. The team leader, Jyl Stoker, berates her strong but gentle explosives expert, “Bunny” Cheung, for the accident, and accuses him of letting thoughts of his family at home distract him from his real work. Bunny never wanted to leave them, and only accepted this job because Stoker called in an old debt. She concedes that she’s gone too far, but the grim atmosphere is getting to everyone; according to Vega Jaal, the planet Akoshemon is legendary for the cruelty and barbarity of its people, who committed every atrocity known to sentient species. Jaal, whose people have a nearly psychic affinity with geology, can sense a terrible darkness lurking deep within the moon...
Stoker shows the Doctor a permit from the University of Tyr, apparently proving that she and her fellow “archaeologists” have the right to be here, but as soon as he’s sure that Nyssa is recovering the Doctor reveals that he knows the permit to be a fake. Stoker and her team are really independent miners who want to stake their claim to the moon before it’s jumped by a rival consortium. The Doctor assures Stoker that he has no interest in jumping her claim, and even helps her to repair her damaged scanners. Once they’re up and running, they detect rich deposits of lexium, enough to make Stoker and her team-mates rich for life. The team throws a party to celebrate their fortune, but Vega Jaal senses death waiting in the tunnels and leaves the party early, convinced that they will all die if they don’t leave the moon at once. Tegan rejects a pass from the shy Jim Boyd to care for Nyssa, who is recovering from her concussion but can sense some evil force lurking in the shadows...
The Doctor follows Jaal into the tunnels to confront him, and they find an ancient door which had been hidden by the darkness. The party grinds to a halt upon news of the discovery; if the moon turns out to be sacred ground, they will lose their mining rights. Stoker reluctantly agrees to investigate, and with Bunny’s help, they break open the door and enter. Beyond they find a fully equipped laboratory which was being used to research suspended animation systems -- but it was apparently abandoned in a rush, yet locked from the inside. Realising that their discovery will delay the start of mining, and that it’s going to be some time before he gets to see his family again, Bunny copies the last holographic message from his young daughter into a recorder built into his ring.
The Doctor calls Vega Jaal into the laboratory to see if he can sense anything, but the alien miner is nearly overwhelmed by the sense of evil in the room. Jaal senses a hollowness behind a nearby wall, and the Doctor finds that the wall opens up into another room containing five human bodies which appear to have been drained of blood. He returns to the main laboratory to look up the base’s personnel records, but while he and the others are occupied, Vega Jaal slips back into the room containing the corpses. Moments later, the others hear a scream, and find Jaal’s withered body lying with the others. The Doctor realises that Jaal had accepted his fate and decided to face it, hoping either to defeat it or at least give the others a warning they couldn’t ignore. Nyssa suffers a heart attack, overwhelmed by the sense of evil around her, and although the Doctor revives her with CPR he is shaken by the near loss. Nevertheless, Nyssa is now his only link to the psionic force which drew them here, and despite the risk he may have to take advantage of her connection to the evil in order to find and defeat it.
Bunny wants to send out a call for help, but Stoker convinces him to hold off, fearing that any such call will be picked up by a Consortium vessel which will jump their claim. Bunny soon has cause to regret agreeing with her when their team-mate Nik is found dead in the tunnels, his body drained of blood. Whatever killed Vega Jaal is not confined to the laboratory after all.
The Doctor studies the lab’s computer records and matches names to six of the five bodies; only Technician Ravus Oldeman is missing. Tegan points out that Oldeman may be “preserved” in one of the suspended animation systems the lab was testing. The Doctor, furious with himself for overlooking this obvious possibility, realises that the psionic field which is affecting Nyssa is subtly influencing everyone else as well, including him. He returns to the room where Vega Jaal died, finds Oldeman in a suspension tank, and revives him. Meanwhile, Nyssa rests and dreams of stepping out of the TARDIS into a vast darkness, where a gloating, evil voice tells her that this is the void left behind by the destruction of Traken -- and that her blood runs black with its corruption.
Oldeman wakes, terrified and disoriented, to find that he’s aged physically because he entered the tank in a rush without checking its systems properly. The Doctor must give him a dose of neurolectrin to stabilise his neurochemistry; Oldeman will require further doses to stabilise fully, but if he takes too much he will become addicted to it. Once he’s settled down, Oldeman identifies himself as a junior technician who was working on a project to create an Akoshemon-human hybrid. Although the project leader, Garondel, didn’t believe all of the legends about the evil planet, he did believe that the people of Akoshemon had longer-than-average lifespans; by using samples from the dead world, he hoped to find a way to extend the average lifespan of the human race. But the monstrous hybrid they created turned out to be more powerful than they imagined, and only Oldeman survived its attack. He’s been in hibernation for over 150 years... but it seems the creature is still alive and feeding.
Bunny has had enough and returns to the main cavern to send out a distress signal. Tegan and Jim follow him, but Jim lags behind -- and although Bunny and make it to the cavern safely, Jim is attacked by the monster. Tegan and Bunny hear him scream and arrive just in time to see the monster retreating from Jim’s wasted body. Tegan does not stop Bunny from sending the distress call. When Stoker learns what he’s done, she is furious and refuses to speak to Bunny -- even though they are now the only two survivors of their team. Meanwhile, the distress call is picked up by Silas Cadwell, second-in-command on the Consortium ship Adamantium. The Adamantium’s captain, Lawrence, has a history with Jyl Stoker, and he realises that if she’s risking her claim the situation must be desperate indeed.
Upon arriving, Lawrence takes charge of the situation and sends out a patrol to find and kill the “Bloodhunter”. The Doctor fears that this is more than a simple bug hunt, but he and Bunny accompany the patrol -- and Bunny is attacked and nearly killed by the Bloodhunter. As the Consortium troops open fire on the Bloodhunter, it tries to drag Bunny down the tunnel, but the Doctor, having already noted Bunny’s inhuman strength and dexterity, saves him by breaking off the arm which he has deduced is bionic. The Bloodhunter retreats into the tunnels, taking the bionic arm -- and with it, the holographic record of Bunny’s daughter, which was powered by the bionic arm’s energy cell. Bunny returns to the Consortium ship for treatment, where Stoker, shaken by her friend’s close call, finally lets the danger sink in.
The Consortium troops are confident that the Bloodhunter can’t have survived the barrage of blaster fire, and Nyssa has sensed its death, but the Doctor still believes that something even worse is lurking elsewhere on the moon. He hypnotises Nyssa, and when she enters a trance, the room seems to darken around her; the Doctor moves his hand into the darkness, and experiences a vision of himself suffering multiple deaths throughout his remaining regenerations. He advises Lawrence and Stoker to give up and go while they still can, while he and his friends remain to face the evil, but they are suspicious of his motives. Lawrence, however, admits to Stoker that he’s also suspicious of Cadwell, who recently transferred to the Adamantium and seems just a bit too good to be true.
Lieutenant Crook and his men find the Bloodhunter’s body, and the Doctor and Cadwell agree that it should be brought aboard the Adamantium for further study; however, Cadwell has no intention of letting the Doctor participate in the post-mortem, apparently regarding him as a rogue miner and therefore beneath contempt. But the Bloodhunter revives, killing Crook and the two other crewmen carrying its body back to the ship, and the Doctor remembers too late that the whole point of the experiment was to create a being with an extended lifespan, capable of sending its body into a deep metabolic coma. Lawrence sends out more patrols to find and kill the creature for good, but, shaken by the deaths of his men, he allows Stoker to convince him to look up Cadwell’s personnel record and find out if his suspicions are legitimate. Stoker is interested to note that Cadwell recently transferred from the Titanium, a ship on patrol in the same sector where she received the anonymous tip which first directed her here...
Bunny, fearing that he’ll never see his family again, tries taking over the bridge at gunpoint, demanding to be taken home. The Doctor, Tegan and Stoker manage to talk him down, and Lawrence promises not to press charges. Shaken by what he’s just done, Bunny leaves the ship to cool down, and Tegan follows -- but as soon as they leave the safety of the ship they are attacked by the Bloodhunter. Bunny pulls it off Tegan, saving her life, but this time it drains him completely before the Consortium troops arrive and drive it off. Stoker and Tegan take Bunny’s death hard, but the Doctor is more concerned with its odd feeding patterns; it is attacking too often, and draining too much blood, for something which apparently survived 160 years with no food. He fears that the evil it serves attacked the TARDIS because it was after the Doctor himself -- and he also fears that, like everyone else on the moon, he is subconsciously being influenced into making decisions that will serve the evil without realising it.
Despite the risk, the Doctor hypnotises Nyssa again and uses her psychic link to the evil to track down the Bloodhunter. Tegan remains on the ship and watches over the sleeping Oldeman, who has been taking too much neurolectrin and, as the Doctor feared, has become addicted to it. Meanwhile, Stoker admits that she’s still in love with Lawrence, even though he stayed loyal to the corporation which funded their college education while she struck out independently. She convinces him to use his security override to break into Cadwell’s personal files, but they find that Cadwell has hidden away even more secret files under a second level of encryption. All they can decipher is the file name: “The Dark.”
The Doctor and Nyssa return to the laboratory, where a closer examination of the room reveals a passageway hidden in the shadows. The passage leads deeper into the caves, through tunnels lit by glowing worms and a vast cavern filled with stalactites and stalagmites, into a cavern with a large black pit filled with a substance which seems to radiate evil. Runes carved into the mouth of the cave tell the story of men who once landed on Akoshemon and fought a legendary being of immense evil, burning it to ash and burying its remains in this moon. The Bloodhunter then enters the cavern and regurgitates blood and bile into the pit, and while it is doing so, the Doctor and Nyssa flee, realising that it is feeding its master.
Back at the Adamantium, Nyssa collapses from exhaustion as the Doctor tells Tegan what he’s seen; Cadwell listens in, but apparently dismisses the Doctor’s story as nonsense. Tegan then informs the Doctor that the drug-addled Oldeman has been raving deliriously in his sleep, and that it seems he’s no mere lab technician after all. When Oldeman wakes, the Doctor forces him to admit that he was in charge of the project all along, and that he altered the personnel records before entering hibernation, fearing that people would learn he deliberately released his own creation upon the others just to see what it could do. The Doctor takes this news to Lawrence and Stoker, just as Cadwell accesses his private records, thus enabling Lawrence to read them as well. As Stoker had suspected, Cadwell sent her the anonymous tip, sending her team into danger and waiting for her to send a distress call to Lawrence’s ship, just in order to get himself to Akoshemon’s moon. The Doctor realises too late that Cadwell believed every word of his story, and returns to the sickbay to find that Cadwell has kidnapped Nyssa, the only person who can lead him to the pit where the ashes of the Dark were buried.
Fearing that Cadwell intends to resurrect the Dark, the Doctor leads a patrol of Consortium troops to the pit, but advises them to set their weapons to stun in case they get involved in a firefight in the dark. He also insists that Oldeman accompany them to see for himself what his arrogance has unleashed, but as they approach the pit, Oldeman begins to suffer neurolectrin withdrawal and the Doctor comes to have second thoughts. Nyssa has been struggling, delaying Cadwell’s progress, and the Doctor catches up to him just in time to stop him from emptying a container of liquid into the pit. But it’s Nyssa who delivers the blow which knocks Cadwell out -- and the Bloodhunter then attacks Oldeman, rips out his throat and casts his blood into the pit. Nyssa vomits out the darkness within her as the Dark rises from the pit, corporeal at last. The Doctor and his companions fleet, but most of the Consortium troops are killed as the Dark envelops and consumes them. The Doctor manages to seal the laboratory door behind him, but the Dark hammers at it, trying to get through, and he knows it will eventually succeed...
Back on the ship, the furious Cadwell reveals that he is descended from those who entombed the Dark in this moon -- and that he was trying not to resurrect it, but destroy it. Nobody knows what the Dark is; some believe it is all that remains of the void before Creation, the cauldron in which the forces of evil were first spawned. Shredded by the Big Bang, the remnants of the void coalesced around the world that became Akoshemon, dooming the world to a history of evil and corruption. Cadwell’s ancestors used light to weaken the Dark and flames to burn it to ash, but it lived on as a psionic field, influencing the minds of others and engineering the creation of a monster which could bring it blood with which to bind its ashes together and give it corporeal form once more. Cadwell didn’t reveal his true agenda for fear that the others could have been influenced by the Dark -- as was Nyssa when she struggled against him, and as was the Doctor when he took Oldeman to the pit and thus provided the Dark with the blood it needed to complete itself. Now the Dark is fully corporeal again, and no one is safe.
Lawrence prepares to evacuate, and the Doctor tells Tegan and Nyssa that they must all leave with him; this evil is too strong for them to fight, and once they’re safe he will summon the TARDIS by remote control. Once he’s sure they’ve accepted this, he leaves the ship, determined to get his friends to safety while he confronts the Dark alone. The Adamantium takes off, but at the last moment, Lawrence is possessed by the Dark and shoots out the autopilot, causing the ship to crash back down to the surface. Lawrence is mortally injured, and Stoker is forced to leave him behind as the bridge is engulfed in flames.
The crash damages the tunnel complex and cracks open the laboratory door, and the Dark begins to seep through. The Doctor flees and helps rescue Stoker, Tegan, Nyssa and Cadwell from the burning wreck of the Adamantium, but Cadwell believes that he’s only condemned them all to a slower and more painful death. As soon as the flames die down, the Doctor sends Stoker and his companions back to search the wreck for zenesium flares, which might be powerful enough to stun the Dark at the very least. The wreck is unstable, and Nyssa falls through a hull plate while trying to reach a flare. Stoker returns to the caves with the flare while Tegan searches for Nyssa, but Nyssa has already been found by Lawrence, who survived the crash but is hideously burned over most of his body.
The Doctor deduces that the Dark can only achieve full physical existence in the total absence of light -- but it has the ability to absorb light into itself, and as the Doctor and Cadwell wait for Stoker, the lights in the cavern grow dimmer and go out completely. Stoker arrives and triggers the flare just in time to save the Doctor, but the Dark has consumed Cadwell, who gives the Doctor his gun and advises him to use it on himself before it’s too late. Cadwell’s body then crumbles apart, consumed from within. The Doctor calls Tegan and orders her to come back to the caves, but she refuses to leave Nyssa behind. Frustrated, the Doctor lashes out at Tegan’s stubbornness, and Stoker notices a dark shadow on his cheek -- or under it. The Dark touched him a moment before she arrived, and it’s eating away at him from within, making him fear for his friends’ lives and doubt his own decisions.
The Doctor searches the laboratory for neurolectrin, but realises that he doesn’t know why he needs it. Does he have a plan he’s shielding from himself so the Dark can’t detect it, or is the Dark influencing him for some reason? The Dark begins to seep back into the laboratory, and the Doctor and Stoker flee in the only direction they can, towards the pit where the Dark was reborn. Tegan arrives in the lab too late to follow them, and tries locking herself in the stasis tank to escape the Dark -- but the Doctor and Stoker hear the sound of the tank being opened, and hear Tegan screaming before communications cut out completely. The Dark surrounds Stoker and the Doctor, but while Stoker holds it at bay with the feeble glow of her cigarette lighter, the Doctor gives up hope, believing that all of his companions are now dead.
In fact, Tegan is still alive; it was Nyssa and Lawrence who opened the stasis tank. The dying Lawrence begs the girls to take him to Stoker, and they head into the tunnels, where they see a faint light and find Bunny Cheung’s bionic arm playing back the holographic recording of his daughter. The hologram lights their way forward, driving back the Dark, and they are reunited with the Doctor and Stoker just as the Doctor is about to shoot Stoker and then himself to save themselves from the Dark. Galvanised by the return of his companions, the Doctor realises what he was about to do and throws away the gun, vowing to stand and fight. However, on the way back to the pit, Lawrence finally succumbs to his horrifying burns and dies.
The Doctor, Tegan, Nyssa and Stoker return to the pit to find the Bloodhunter lurking almost pathetically in the cavern, as if it’s realised its master no longer needs it. The Dark enters the cavern and coalesces into a shadow duplicate of the Doctor, intending to use their psychic connection to possess the TARDIS and spread its influence over all time and space. However, the Doctor realises that it wants something else first, and realises the truth; since it used Oldeman’s blood to complete its physical form, it acquired his addiction to neurolectrin. The Dark attempts to force the Doctor to inject the neurolectrin into himself, intending to have the Bloodhunter drain the blood from the Doctor’s body and feed it.
The Doctor begs the Dark to remove its mark from him, promising to inject himself of his own free will if the Dark promises to spare his friends. Amused, the Dark does so, but once the mark is removed from him the Doctor injects the neurolectrin into the Bloodhunter instead. The Dark attacks the Bloodhunter and tears it apart, but while it is distracted Stoker shoots it repeatedly. It attacks her and snaps her neck, but the shots have weakened it; now that it has confined itself to a corporeal form, it can be killed. The Doctor kicks the Dark back into the pit, uses Stoker’s lighter to set Bunny’s bionic arm on fire and flings it into the pit, where its power cell explodes, burning the Dark’s remains to ash and destroying it forever. The Doctor, Nyssa and Tegan return to the TARDIS and depart, having defeated the Dark, but mourning the deaths they were unable to prevent.