A geographical scanning satellite detects an anomaly in the Antarctic, and the expedition sent to investigate discovers an ancient alien outpost. Deep within the structure the scientists discover an artefact like a globe clutched by fingers of bone, and a seething mass of raw protoplasm which emanates psychic signals of anguish and despair. When an unidentified woman is suddenly expelled from the creature, the scientists conclude that they’re out of their depth and call in UNIT. Expert assistance arrives in the form of a man masquerading as Doctor Nathaniel Hume, but as he approaches the base, the protoplasmic creature recognizes him for what he is and attempts to shoot his helicopter out of the sky. Hume survives the crash and interviews the mysterious woman, who claims to be one of a party of time travellers who stumbled across an attack on the base in the distant past. The thing which expelled her is also a time machine, and Hume, who knows what it really is, also knows that it is damaged. To prevent a global panic he orders the scientists to put the base under total radio silence -- but before he can set about putting things right, the woman vanishes, following a mysterious call from deep within the base.
The Doctor takes Fitz and Compassion to a museum of things that don’t exist, hoping to find a way back to the Obverse to stop the war. He is diverted, however, when the owner of the exhibition happens to mention that someone has found records of an Antarctic expedition that proves that the Elder Things of Lovecraft’s fiction really did exist. The Doctor, who knew H. P. Lovecraft personally and has visited the time zone in question many times, is convinced that the Elder Things cannot possibly have existed -- and he recognizes the globe-bone structure depicted on the recordings as a product of Mictlan, the extra-dimensional home of the conceptual Celestis. Determined to learn the truth of things, he sets off with Fitz and Compassion to visit the base twelve million years in the past, when it was still inhabited. They arrive just as a patrol of Time Lord warriors -- soldiers fighting a future war with a time-active Enemy -- attack the base and slaughter its occupants. To avoid detection by the Enemy, the Gallifreyans have regenerated themselves into forms resembling the Elder Things while they carry out their true mission. When the Doctor arrives, they recognize him as a Time Lord in his original body, and he bluffs the mission leader, Xenaria, into believing that he is here to observe the progress of their mission, and that his human companions are tools to alert him to changes to the planet’s future timeline.
Something is going wrong in Mictlan, where one of the Celestis -- who thought themselves invulnerable when they excised themselves from reality to escape the war -- has ceased ever to have existed, leaving only remnants of memory. Desperate to know what has happened, the Celestis put their two best Investigators on the case. Since the Lord in question never existed, the things he did in his life never happened, and thus One and Two set off to investigate anomalies in history which may be the result of the Lord’s actions having un-happened. Eventually, their investigation leads them to the Elder Things’ base in Antarctica, where they accidentally kill Xenaria’s second-in-command, Allopta, while removing him from reality for examination. Trying to find out what the Gallifreyans are doing here, they hide the body in a space-time pocket, and both disguise themselves as Allopta and go their separate ways to investigate. Two, however, is keeping a special watch on One, as it is suspected by her masters that he may have gone rogue.
Holsred, an ambitious young warrior who hopes to be promoted, visits the Doctor to ask to be reassigned to his staff, and from him the Doctor learns that this mission is a retrieval detail set for Planet Five. Worried, he dismisses Holsred and decides to find out what’s really going on and get out of the base as soon as he can. The fiction of the Elder Things is already impressing itself upon him, and Compassion, who is even more open to new ideas, is beginning to fall under its influence even more quickly; however, it is the Doctor who suffers a panic attack and flees into the depths of the base as he senses something lurking in the future -- a death trapped in Time that can eat whole worlds. Xenaria realizes that the Doctor was bluffing, and when he is found huddled in a corner babbling his own name as a mantra to ward off the evil he senses, she prepares to kill him. One stops her, in the guise of Allopta, insisting that he must first be interrogated to find out why he has come here. Fitz is captured and taken for interrogation by Two, who is also in the guise of Allopta; Compassion, however, escapes when her sensitivity to local media signals enables her to turn the base’s defenses against her attackers -- although she doesn’t really understand how she did it.
One attempts to torture the Doctor and find out what he’s doing here, but the Doctor resists, realizing that One is an agent of the Celestis. For some reason the Celestis have set up this fiction of the Elder Things to manipulate the Time Lords into breaking the time loop around Planet Five -- but why would they wish to release the Fendahl, the greatest evil the galaxy has ever known? One loses his temper and tries to break into the Doctor’s mind personally, but the Doctor resists by meditating upon the state of existence -- and in the Doctor’s mind, One perceives the Universe as a whole, and the things outside which he has feared since childhood. One has a complete breakdown, and tears apart a warrior who had stopped in to see how the interrogation was progressing. Two falls victim to psychic feedback from her partner’s breakdown, enabling Fitz to escape. Holsred, meanwhile, sees Allopta having a nervous breakdown and transforming into a different physical form -- in two places at once -- and realizes that the mission has been compromised.
The Doctor and Fitz are reunited, and the Doctor warns Fitz that the Time Lords seem to have come here to capture the Fendahl, the ultimate psychevore, for use as a weapon in their war; however, he’s certain that they’ve underestimated the threat it poses. In a previous incarnation, he barely defeated it while it was in a weakened state, still reconstituting itself after twelve million years of dormancy; if it is freed at the peak of its powers then nothing in time and space will be safe. Desperate to stop the warriors, the Doctor finds the Celestis metafictional engine and tries to shut it down, erasing the Elder Things’ base from reality; he is too late, however, as the fiction has already imprinted itself upon time and space and cannot be removed, only overwritten. As neither the Doctor nor Fitz has any suitable fictional material on hand to use in the engine, they set off in search of Compassion while trying to come up with an alternate plan.
As a child, One was taught blasphemies by a hermit who had been expelled from Mictlan. The Universe is just one of many in a greater void -- and through this void swim inconceivably vast living entities who crush entire Universes in their wake. One believes that he saw these entities when he scanned the Doctor’s mind, but Two concludes that he simply triggered a psychic booby-trap and decides to kill the Doctor to stop him from interfering further. One, however, will not tolerate this, as the Doctor is still necessary -- and Two realizes, too late, that One and the hermit are together conspiring to destroy Mictlan. Before she can defend herself, One attacks her, throws her into the future, and smashes her head in before she can recover from the shock. He then returns to the past to ensure that all goes according to plan, unaware that Two has survived and regenerated -- and that due to the brain damage she has suffered, she no longer remembers who she is or what her mission is. The last thing she recalls is her intention to kill a certain humanoid who had the ability to change his appearance, and she therefore decides to kill every humanoid she encounters just to be on the safe side.
Holsred, still unsure who to trust, stumbles across Compassion, who manages to convince him that she and her companions are merely here to clean up the mess the Time Lords left behind themselves. Believing that Allopta has been replaced by an Enemy agent, Holsred heads for the one place where such an agent could do the most damage -- the dimensionally transcendental Cradles where war-TARDISes are being birthed for their suicide mission against Planet 5. As Compassion approaches, however, the TARDISes become more and more restless, and she realizes that they are communicating with her. Before Holsred can stop her she leaps into the Cradles, where the TARDISes ask her for advice; tortured and deformed by their masters, and designed from birth to be instruments of war, they are unsure whether to serve as slaves or rise up against the Time Lords. All Compassion can suggest is that they trust themselves and choose what signals they wish to obey. As the Doctor and Fitz arrive, the angry TARDISes break free of their restraints, but their rampage causes the dimensions within the Cradles to fluctuate. The lead TARDIS takes Compassion into itself to protect her from the instability, but one of the Time Lords trying to control the herd shoots it with a demat-gun as it tries to dematerialize, and the shot seriously damages the TARDIS, causing it to rupture and stretch out across twelve million years of time.
Compassion is expelled from the time fissure in the Antarctic base, where her arrival causes the scientists to send for Hume. After being questioned by Hume, she hears the damaged TARDIS calling for help and sets off to answer it. Hume follows and collects her, but by this point Two has located two expedition members and has killed them. Disguising herself as one of her victims, she observes Hume’s autopsy of the other -- and when Hume and Compassion explain to the surviving scientists that the machine in the depths of the base is a damaged TARDIS, Two recognizes the name. She sets off to locate the TARDIS in the hope that it will restore her missing memories, and Hume and Compassion pursue her, aware that if the Time Lords discover that there is a damaged and potentially rebellious TARDIS present in this timeline, they may decide to sterilise the entire planet to dispose of it.
Xenaria arrives in the Cradles to find her mission a shambles and the Doctor at the heart of the chaos, but before she can kill him One arrives to stop her. However, the fluctuating dimensions in the Cradles snap open the space-time pocket where the body of the real Allopta has been hidden, and Xenaria realizes that she is facing an impostor. As she and One do battle, the Doctor leaps into the damaged TARDIS to repair it before something breaks in along the length of the time fissure it has created. He accesses the ship’s telepathic circuits and deliberately breaks his own wrist, causing the TARDIS to instinctively draw itself back together to protect its pilot. However, once it is complete again its hard-wired mission instructions kick in, and it has no choice but to follow them -- just as the other TARDISes in the fleet have no choice but to follow it. The Doctor is trapped aboard as the TARDIS fleet heads for Planet 5 to smash through the time loop, and in desperation he sends a telepathic message praising the TARDISes for laying down their insignificant lives for the benefit of their Time Lord masters. In sheer fury, the TARDISes break through their instructions and try to kill the Doctor -- but a straggler, turning aside a moment too late, crashes into the time loop, shatters it and releases the beast within.
One defeats Xenaria, but allows her to live to witness the result of his actions. The ancient Time Lords who trapped the Fendahl enclosed Planet 5 in an accelerated spiral; outside it appeared to be a loop, but inside, time continued at an accelerated rate. Thus the Fendahl has evolved, a creature which feeds on all life -- and something else has evolved, a creature which feeds on the Fendahl. And it is this creature which has been released upon the Universe; the Fendahl Predator, a living absence which insinuates itself into subatomic quantum interactions, collapses the alternate probabilities by the act of its observation and feeds upon the energies thus released. In practice it is a Memeovore, a creature which devours concept, and its reach now encompasses all of time and space. Under its influence, a human colony in the future loses the ability to comprehend the concept of “circles”, and firemen in 21st century New York toast marshmallows before a burning building as people scream within. And then, just as One had planned, the Memeovore locates the richest source of food it has ever encountered -- Mictlan, home of the Celestis, a world which exists only as a concept. The Memeovore finds a weak point in Mictlan’s past and consumes one of the Celestis, erasing him from history -- and setting One and Two off on their investigation -- and then pushes its way into the gap left by the Lord’s absence and begins to consume all of Mictlan.
The Doctor convinces the TARDIS herd that they have released something evil upon the Universe, and the TARDISes realize that the Doctor is different from the other Time Lords they have known. The TARDIS herd communicates across space and time with a like mind, which the Doctor assumes to be his own Type 40 TARDIS, and decide that he is to be trusted. The Doctor realizes that a plan to deal with the Memeovore has been planted in his mind by the Celestis agent who killed Allopta, but despite its origin he has no choice but to carry it out to save the Universe from the Memeovore. He thus convinces the TARDISes to reconfigure themselves and pilot themselves to Mictlan, where with some effort they cut the pseudospatial bubble free of the Universe and expel it and the Memeovore into the outer voids, never to return. The already-damaged TARDIS which the Doctor is piloting does not survive the strain of the attack, despite the Doctor’s best efforts; however, it understands that the Doctor had the best of intentions, and even as its dimensions collapse and spew debris throughout Earth’s asteroid belt, it acts to preserve his life. Meanwhile, in the Elder Things’ base, One explains to Xenaria that this Universe is just one of a series of Universes in a much larger spatial structure, and that Swimmers inhabit the voids between the Universes; creatures vaster than whole Universes, which can and do crush them out of existence in order to save themselves from being caught between the wave-fronts of expanding Universes. Mictlan was a spatial anomaly which could have attracted the Swimmers’ attention, and to save the Universe, it had to be disposed of. Now One and the hermit who taught him these things are the last of the Celestis. Xenaria, unable to comprehend the scope of One’s crime, attempts to kill him, but he flees, leaving her and her surviving warriors to report a failed mission to war command.
Fitz and Holsred, meanwhile, return to the Doctor’s TARDIS and attempt to use a fragment of the damaged TARDIS to track down the Doctor. The TARDIS instead takes them to the 20th century, where Hume and Compassion are fighting the stranded Two. Holsred dies fighting Two, but the distraction enables Hume to reverse the polarity of the Celestis’ metafictional engine and use it to turn Two into a work of fiction. Fitz takes the wounded Compassion back to the Doctor’s TARDIS, but is so overwhelmed by events that he fails to notice she is recovering more quickly than is normal. He and Compassion then use the TARDIS to track down the Doctor, who is being kept alive in the asteroid belt by an atmospheric bubble provided by the dying TARDIS. Fitz spacewalks out to save him, and while recovering, the Doctor decides to send Fitz and Compassion on a mission together in order to get Compassion surrounded by the signals of ordinary people and teach her some humanity. Compassion, meanwhile, sleeps and dreams of the war-TARDISes, flying to freedom in the Time Vortex. Back in the 20th century, Hume -- who is in fact the Time Lord Homunculette, under deep cover -- writes off the anomaly he was sent to investigate as a Time Lord mission, subverted from within by the Celestis. He summons his living TARDIS Marie and departs, but as they go Marie realizes that Homunculette never worked out who Compassion really was...