The Doctor and Ace are on their way to pick up Benny from the Orbos research facility, in orbit around the planet Marran Alpha, when the TARDIS telepathic circuits are overwhelmed by a cry for help from the Doctor’s old friend Remnex. The Doctor and Ace both experience a vision of dark, burning black flames before the cry finally ceases. Disturbed, the Doctor tells Ace that Remnex is one of three scientists stationed on Orbos and conducting experiment with black light -- not ordinary ultraviolet light, but the energy generated by quantum meta-fluctuations within the space-time continuum. It seems that Remnex has paid the price for tampering with such a dangerous energy source.

In fact, Remnex is still alive and well, and is on the observation deck of Orbos, looking out over the dead world Marran Alpha. The unpleasant Professor Slyde scoffs at Remnex’s romantic description of the cosmos; Slyde has trained himself to see everything in purely scientific terms, and regards looking at the view as a waste of time when Remnex should be working on the station’s solar generator. Nevertheless, Slyde is intrigued by Remnex’s description of the legendary Doctor, especially when Remnex adds that Professor Lomar believes the Doctor could help them in their experiments. Lomar and Benny are shifting equipment while waiting for the Doctor to arrive, but Benny is concerned by the absence of her friend Victor Farrison. Victor had arranged to meet her here on Orbos, but never showed up, which isn’t like him at all...

In fact, Victor and his android servant Joseph are in the death pit of Marran Alpha, clearing away the remains of fanatics whom it’s said were buried alive centuries ago. After two weeks of excavation they’ve finally found what they’re looking for -- a human skull which, although thousands of years old, still feels almost alive in Victor’s grasp. Their mysterious employer, a man named Broke, demands that Victor hand over the skull, but Victor, who has been forced to work against his will, refuses to do so unless Broke explains what this has all been about. Instead, Broke strikes him down, knocking him out and taking the skull from him. Joseph fears for Victor’s life, but Broke scoffs at this show of concern, dismissing Joseph’s “personality” as a programmed facsimile of his creator’s. The skull is far more important, for Broke is a loyal servant of the Dark Flame, and this is all that remains of a man named Vilus Krull.

Benny, Slyde, Lomar and Remnex wait in Lomar’s office for the TARDIS to arrive, and when it does, the Doctor is delighted -- but disturbed -- to find Remnex alive and well. The Doctor sends Ace and Benny to amuse themselves while he chats with Remnex, catching up on old times, telling him what’s happened to Mel, and asking almost casually whether Remnex has access to any teletemporal projection equipment. He hasn’t, but Lomar then asks the Doctor if he’d advise them on their attempt to cause a controlled black light explosion. Disturbed by the thought of such a risky experiment, the Doctor agrees to check out the laboratory equipment, including the isochronyte crystal they’re using as a control element. The crystal is temporally unstable, but Slyde assures him that it’s only meant as a temporary measure until a more suitable control element can be found, one that exists partially outside the space/time continuum. Learning that Remnex is in charge of the initial stage of the experiment, the creation of an artificial sun which will provide energy for the black light explosion, the Doctor decides to have another chat with him...

Ace is amused to learn that Benny has been spending the last two weeks dumping the station’s rubbish into its waste disposal unit, a one-way transmat which sends all of the rubbish to the volcanic, acid-drenched surface of Marran Alpha. The transmat system is a shoddy affair which Ace fears could be leaking exotic particles, and when Benny collapses from a sudden migraine, Ace initially believes it to be a side effect of prolonged exposure to the transmat. But when Benny experiences a painful vision of burning, dark flames, Ace recognises it as the vision she and the Doctor experienced in the TARDIS -- and then hears someone scream in the distance.

The Doctor recognises the sound of Remnex screaming, but when he arrives he finds the door to Remnex’s cabin locked. Lomar and Ace also arrive, and Ace smashes the door down to find Remnex lying dead on the floor, stabbed through the eye into the brain. Slyde and Benny also arrive as the Doctor studies Remnex’s body and finds that he’s holding the isochronyte crystal, which he presumably used to transmit the cry which the Doctor and Ace heard in the TARDIS. Benny is upset to learn that the Doctor knew Remnex was in danger but did nothing to save him, and when the Doctor describes his vision of a dark flame, it reminds Benny of a cult which used to exist in this part of the galaxy -- the Cult of the Dark Flame, which worshipped an energy being from another universe. The cult supposedly died out centuries ago, but perhaps it’s still active after all...

Sadly, Lomar confirms that the transmat has been used recently. The Doctor takes Ace to the sickbay, as Slyde shot her with a neural stunner before disposing of Benny; fortunately, Ace’s combat suit diffused the full effect of the blast, but she remains disoriented and delirious, and babbles about Benny and the power of the Dark Flame. The Doctor hypnotises her, putting her to rest; now he must find Slyde.

However, Slyde is no longer on Orbos, having used the transmat to send himself and Benny not to the surface of Marran Alpha but its underground caves. Slyde and Broke lock Benny up in a cell with Joseph and the recovering Victor, but it turns out Slyde won’t need another archaeologist after all, as Victor has finished his work and found the skull. Satisfied, Slyde transmats back to Orbos and brings back the body which will be used as the new host for the resurrection. He and Broke then fetch their prisoners to witness the ceremony, and although Benny tries to remain flippant this becomes difficult when she sees Slyde and Broke drop Remnex’s body onto an ancient altar. Slyde admits that he killed Remnex because the old man discovered that Slyde followed the Cult of the Dark Flame -- and now Slyde intends to use the skull to resurrect the Dark Flame’s emissary. Benny scoffs at Slyde’s mad beliefs until Slyde uses the skull to raise Remnex from the dead. But the mind inhabiting Remnex’s body is now that of the Emissary...

The Emissary takes a moment to collect himself, as he has been dead for generations and needs a moment to adjust to his new body. He is disappointed in Slyde for providing him with such a feeble old corpse to inhabit, especially one which has been stabbed through the eye, but when Slyde assures him that Remnex died in agony, the Emissary decides to let this pass. Benny and Victor have seen enough, and make a break for it while Slyde and Broke are distracted by their master’s resurrection; unfortunately, they aren’t distracted enough, and Benny and Joseph are unable even to get out of the cave. Victor seizes the skull and flees, but Slyde shoots him with the neurostunner at full power. Gravely injured, Victor crawls back to the transmat...

The Doctor and Lomar return to the scene of Remnex’s murder to investigate further, but find only that Remnex’s body has gone missing. Despite Lomas’ reservations, the Doctor decides to wake Ace up to help investigate, and despite the intense sleep she’s fallen into, he eventually snaps her out of it by calling her Dorothy. While Lomar searches the lab for clues, the Doctor and Ace discuss the situation, but as they talk they encounter Victor, who has reached Orbos and is crawling along the corridor with the skull. The combination of the neurostunner blast and the transmat process proves to be too much for him, and he dies after handing over the skull. The Doctor convulses when he touches the skull, as he is time-sensitive and the skull is parachronic, existing partially outside the space/time continuum. He thus gives it to Ace for safekeeping, but remains concerned by its nature -- especially considering that the Cult of the Dark Flame was said to worship a being from a universe outside the space/time continuum...

The Doctor sets off to follow a hunch, telling Ace to guard the skull with her life. He has guessed correctly that the transmat is being used to transport more than rubbish, and he uses it to transport himself to the caves in search of Benny. Unfortunately, Joseph lures him into a trap, and the Doctor is thus reunited first with Remnex -- or rather, with the Emissary of the Dark Flame...

Ace refuses to tell Lomar and Slyde where she’s hidden the relic, and realises that they can’t afford to kill her until they know where it is. She thus tosses a smoke grenade at them to cover her retreat, and after some effort they track her down in the main laboratory, near the black light converter. There’s only one way out of the room, but if they attack Ace she’ll use her smart bombs to destroy the laboratory. For the moment, they are at stalemate.

Broke locks up the Doctor with Benny and Joseph, who apologises for leading him into a trap but explains that Broke had threatened to kill Benny if he didn’t. The Doctor accepts the apology and begins hammering on the door, demanding to speak to someone. Just as he’s about to suggest playing I Spy, Broke finally shows up to fetch him for an audience with the Emissary, and the Doctor demands that Benny and Joseph be allowed to accompany him. The Doctor and Benny mock the Emissary’s reliance on a decaying corpse to hold his spirit, but the Emissary tolerates their flippancy, confident that he serves a higher purpose than they can imagine -- the Dark Flame, the evil that burns in the heart of every living being. Benny mocks his arrogance and points out that his pathetic little cult died out centuries ago, but the Emissary proves her wrong by raising the bones of his followers from the grave and granting them the unnatural strength of the undead...

Being surrounded by an army of walking skeletons proves somewhat convincing, and Benny shuts up and listens as the Emissary explains that he requires the skull of Vilus Krull, a man who died thousands of years ago. The Doctor must admit to Joseph that Victor died getting the skull to him, and the Emissary, mocking Joseph’s electronically generated grief, demands to know what happened to the skull afterwards. The Doctor refuses to tell him, and the Emissary apparently chooses not to burn the truth from his mind. The walking dead march the Doctor and Benny back to their cell, where the Doctor explains to Benny that the Time Lords believe the Dark Flame to have originated in a pocket dimension forced out of the space-time continuum by the collapse of this Universe. If this is true it originates from billions of years in the future, when the laws of physics are twisted in incomprehensible ways and anything is possible. The parachronic skull could be used to control the black light explosion on Orbos -- and if so that makes the black light explosion even more dangerous than the Doctor had originally thought.

Lomar transmats herself down to the caves to break the bad news to the Emissary; Ace and Slyde are still standing off in the laboratory, and the skull remains lost. The Emissary thus orders the Doctor to return to Orbos, and gives him ten minutes to return with the skull; if he fails or refuses, the Emissary’s skeletal followers will tear Benny apart. The Doctor and Lomar thus return to Orbos, where the Doctor tries and fails to reason with Lomar. She’s worked all her life to harness the power of black light, which led her to the Cult of the Dark Flame, and now she is completely under its thrall. Lomar marches the Doctor into the lab, where he convinces her and Slyde to let him speak privately with Ace for a moment. Ace is suspicious, but the Doctor explains that Benny is in danger -- and assures her that he has a plan.

In the caves, Broke finds Joseph, who is still stunned by the news of Victor’s death. Broke remains unconvinced that the robot feels any real emotion for its creator, but he pushes Joseph too far, and the enraged Joseph attacks him. When he realises what he’s done he is appalled, and offers no resistance as the enraged and gravely injured Broke switches him off. Meanwhile, as the Emissary and Benny wait for the others to return, the Emissary tires of Benny’s constant flippancy and has her look into his eyes to see her own future. She is shaken to see nothing there. She has no future.

To prove that Benny has really given herself to the Dark Flame, the Emissary has his skeletal followers hold Ace down while Benny beats her up. The Doctor begs him to stop, but remains convinced that the Emissary is simply controlling Benny’s mind, forcing her to do these things. The gravely injured Broke arrives, but the Emissary has no further use for him and orders him to repair the damage the Doctor has done to the transmat. As Broke works, the Doctor asks the Emissary to let him follow the Dark Flame just as Benny has allegedly chosen to, but despite the Doctor’s taunting, the Emissary refuses to give him the chance to surrender to evil. Broke completes his work, and the Emissary thanks him by leaving him to die while he, Slyde, Lomar and Benny return to Orbos. There, the Emissary reveals his intentions for Benny; his current body is decaying rapidly, and he intends to kill Benny and transfer his mind into her body.

Before the Doctor and Ace can follow the others to Orbos, Broke destroys the transmat controls; despite being abandoned by his master, he still serves the Dark Flame loyally until death. He dies, but Ace still feels furious and helpless. Nevertheless, the Doctor feels certain that the Emissary refused to let him “join” the Dark Flame because he is in fact controlling Benny’s mind, and possibly Lomar’s as well; he isn’t strong enough yet to control the Doctor without relaxing his grip on the others. Deducing what the Emissary intends to do to Benny, the Doctor tracks down Joseph, reactivates him and enlists his help in locating the transmat controls and repairing the damage Broke caused. As they work, however, the walking skeletons raised by the Emissary realise what they’re up to and attack. Ace holds them off while the Doctor fixes the transmat, but the damage is more extensive than he’d thought; the central omnitronic processor has melted, and the Doctor doesn’t have a spare. Joseph offers to sacrifice his own processor; this will mean his death, but Ace is being overwhelmed by the undead and Joseph knows there is no time for the Doctor to rig up a relay. The Doctor reluctantly opens Joseph’s access hatch, removes his omnitronic processor and installs it in the transmat, and he and Ace escape.

Slyde finishes preparing the laboratory for the “experiment,” and before installing the skull in place of the isochronyte crystal, the Emissary has Benny kiss its dead lips, just so he can gloat. Lomar then places the skull in the converter and activates Remnex’s solar generator, creating an artificial sun. As the star blazes with light, Benny activates the converter, and soon the effect of the reverse photon field can be seen; the star’s surface begins to darken, heralding the coming of the Dark Flame. The Doctor and Ace materialise in the waste disposal chamber only to see the darkening star; the black light explosion has begun, and the artificial star is becoming a gateway to a dark dimension. Soon the Emissary will be able to spread the evil of the Dark Flame to every corner of time and space...

The Emissary’s followers feel the burning chill of the Dark Flame in their souls, and Benny is shaken to see that the hand which operated the converter is now withered and aged. The Doctor bursts in to find that Benny has shaken off the Emissary’s control too late; a black light explosion is about to take place within the space-time continuum, and its effects will be felt simultaneously throughout all time and space. But until the starlight is fully converted to black light, there’s still a chance to stop it. Ace bursts in with a neutron blaster and tries to shoot the Emissary, but he has the power to shut down the weapon with a thought. Amused, he invites the Doctor to try shutting down the reverse photon field, but the Doctor finds himself frozen in place; as the Dark Flame draws nearer, the Emissary’s power increases, and now he can control the Doctor’s mind as well. The Doctor struggles to resist, and to prevent the Emissary from crushing the Doctor’s mind in his grasp, Ace knocks the Doctor out. She and Benny flee, and the Emissary lets them go, certain that they will come crawling back to him -- and unaware that this was all part of the Doctor’s plan. The neutron blaster was only a bluff, and while the Emissary was attacking the Doctor, Ace took the opportunity to get a good look at the black light converter. Now she’ll be ready to act when the time comes.

The Doctor revives as the Emissary crows over his triumph, but though the Doctor admits that he can feel the Dark Flame burning within the star and within himself, he now knows it for what it is. It is a force completely alien to this dimension, and if let loose it will overturn the laws of nature, destroying countless lives and civilisations -- but it has no will of its own. It’s simply a force of nature, and only Vilus Krull, the twisted man who first made contact with it in this Universe, gives it direction. It would be very different if there were another mind in control. Krull refuses to believe this, but the Doctor challenges him to a mental duel to prove the power of the Dark Flame; by placing their hands on the skull, the Doctor and Krull can tap directly into the power of the Dark Flame through the black light converter, and do battle to determine whether Krull really is the Emissary of the Dark Flame or just a pathetic little man with a modicum of control over an impersonal force of nature.

The duel commences, and despite Krull’s efforts, the Doctor is proven correct; the Dark Flame is just a mindless force from the end of the Universe, which twists time and space about itself but has no will of its own. As Krull and the Doctor do battle, Ace and Benny materialise in the lab; after escaping from the caves, the Doctor adjusted the transmat once again so that Ace could transmat directly to the lab later and catch the others off guard. As the Doctor holds Krull back, Benny deactivates the black light converter, and Krull vanishes, screaming, as time folds back on itself. Benny’s withered hand returns to normal, and the star outside begins to shine with proper starlight once more.