The Charrl, a noble race of insects, have travelled from their dying homeworld to the planet Antýkhon, only to find their new home as barren and lifeless as their old. Knowing that her race may be doomed, Queen Ch’tizz has no choice but to ask the mysterious hermit Muldwych for assistance. He agrees to help them, but for his own reasons. Ch’tizz thus uses her mental powers to reach to Earth in the year 1270, where she strikes a bargain with an ailing Scottish lad, extending his life and sending him on a quest to secure the Charrl’s birthright -- and his own. He crosses the world from the courts of Kublai Khan and Elizabeth I, and even back to Culloden, always in the guise of a mystic and astrologer, always one step behind his quarry…

London, 1909. Butcher Ernie Wright is accompanying the young prostitute Lil Nuttall back to her home when a giant insect steps out of the shadows and tears her to pieces. Nobody believes his wild story, and Constable Reg Hawkins nearly arrests him for the murder; however, a mysterious stranger named John Smith intervenes, claiming to be acting on behalf of Wright’s grandchildren -- who have yet to be born. By the time Hawkins recovers his senses, Doctor Smith has gone, leaving Hawkins with his business card and the firm belief that he himself was drinking with Smith and Hawkins at the time the murder took place.

Claiming that he needs a rest, the Doctor shows Benny how to land the TARDIS herself, but when she follows his instructions there is an almighty explosion -- and she wakes up alone on the banks of the Thames in 1909, clutching a strange ebony wand, and lying next to the hollow shell of an empty police box. Fortunately, lodgings and a generous bank account are waiting for her, as if the Doctor had been expecting something like this to happen. Unaware that her every move is being observed by a mysterious organisation called the Brotherhood of the New Dawn, Benny settles into her lodgings on Dean Street. Her landlady, the elderly Margaret Waterfield, was hired by the Doctor to care for his house after her brother Edward mysteriously vanished and his daughter Victoria moved away from England. Benny soon befriends her, but is less well disposed towards Margaret’s odious acquaintance Lord Bellingham, whom Margaret met through her interest in the occult.

Two months pass without incident, and then Benny receives an anonymous package directing her to the East End, where a series of brutal murders have just taken place. The superstitious locals believe them to be the work of the legendary Springheel Jack, and none of them will share their stories with Benny, an outsider to their world. Her questions, however, attract the attention of Russian detective Mikhail Popov, who is investigating the same murders. When a thug attacks Benny in the streets, trying to steal the TARDIS key, Popov helps to drive him off. The thug drops a business card while fleeing, and Benny notes on it the name and address of a bookseller named Jared Khan. She thanks Popov for his help, and learns that he has come to London on the trail of a killer who ripped apart a number of women in St Petersburg several months ago -- including Popov’s young daughter Natasha.

Benny and Popov investigate a commotion in the streets, and find a delirious woman who claims to have been attacked by the devil himself. The locals refuse to help, since she’s a society woman who had come to interfere in their lives “for their own good”. The suspicious Constable Hawkins starts to question Benny and Popov about the attack, but fortunately Popov carries credentials which prove he is a police detective -- as suggested by his former English tutor, John Smith. While Hawkins keeps back the crowd, Benny studies the unconscious woman and finds puncture marks on her arms and a disintegrating piece of chitin in the street nearby. A young street urchin named Charlie Jackson then steals the woman’s necklace, but Benny pursues him and recovers it; however, when she sees the squalor in which Charlie lives, she relents and allows him to keep the necklace, as he obviously has more need of it. She then returns home, to find that someone has searched her rooms -- someone who apparently had no need to break in. Fortunately, the ebony wand is still safe in her bank deposit box, although an elderly woman claiming to be Benny apparently tried to retrieve it earlier and fled when the clerks became suspicious.

Benny decides to visit Jared Khan, and finds that he owns an occult bookshop full of texts on insect life and treatises on the New Dawn. Khan explains that he is a member of a Brotherhood devoted to helping mankind achieve its true destiny, but Benny doesn’t learn anything useful and leaves when she realises that Khan is trying to hypnotise her. She returns home, planning to rest and then return to the East End to investigate further, but arrives to find that Margaret has been savagely beaten to death. Lord Bellingham claims to have heard Benny and Margaret arguing earlier, and policemen in the pay of the New Dawn arrest her and send her to Holloway. There, a prisoner named Rosa attacks her, trying to get the TARDIS key. Benny overpowers her, and is then released thanks to the intervention of Popov and PM Henry Asquith, who was told of Benny’s plight by a fellow club member named John Smith. When Benny learns that fourteen women were slaughtered in the East End the very night she planned to investigate, she actually thinks for a moment that the Doctor may have had Margaret killed and Benny imprisoned to protect her. She soon calms down, and realises that Khan hypnotised Margaret, forced her to search Benny’s rooms and try to steal the ebony wand, and discarded her when she was of no further use in order to get Benny close to Rosa. Nevertheless, Benny is infuriated when white lilies are sent to Margaret’s funeral by an anonymous guest who doesn’t even bother to show up.

Benny and Popov return to the East End, where to Popov’s horror a giant insect materialises in the street before their eyes. He flees in terror, but recovers his courage and returns to help Benny fight it off before she receives anything more than a scratch. Now certain that something unearthly is going on, Benny hires Charlie to help her break into Khan’s workshop, where they find a collection of news clippings about last year’s explosion in Siberia. Benny theorises that the explosion opened a rift through time and space, and that the insects are using it to travel to Earth. The rift first opened in Russia, where they killed Popov’s daughter, but has since shifted to London. Another of the insects materialises in the shop and attacks them, but the terrified Charlie beats it to death with a heavy book, and Benny is surprised to find that its exoskeleton is brittle and worn. Khan and Bellingham then arrive, and although Charlie flees, Benny is captured and taken to the cellar for questioning.

Khan explains that he serves the Charrl, who are indeed planning to migrate through the Great Divide opened between Earth and Antýkhon; but the Divide is already beginning to close, and any Charrl who pass through are weak and soon die. Only the TARDIS can stabilise the Divide, once its interior and exterior dimensions are reunited. Benny realises that the TARDIS sacrificed itself to prevent Khan from getting hold of it, and refuses to help him; he may claim to be helping a noble race which will bring great knowledge to mankind, but she knows that he and Bellingham are just out for personal power. Khan leaves her to reconsider, and Charlie and Popov take the opportunity to break in and rescue her -- just as Khan had expected they would. He knows that Benny has been scratched by a Charrl and infected with their seed -- and soon, she will fall under their control.

Meanwhile, Ace has been stranded on Antýkhon for two months, having woken next to another police box shell which has since fallen into the hands of Muldwych and Ch’tizz. The imperatives of survival have driven the noble Charrl to hunt the humanoid natives of Antýkhon, who are now the only source of food on the planet. Ace saves a group of humans from a Charrl attack, and thus wins their respect -- and the enmity of their humiliated former leader, Seeba. Hoping to get him on her side as well, she proposes a sneak attack on the Hive to rescue his brother Chel from the Charrl’s larder. Fortunately, she understands the structure of the Hives due to a lecture on termite mounds which the Doctor once forced her to attend -- almost as if he was preparing her for something.

Ace’s party enters the Hive through its ventilation tunnels, and are surprised to find it all but deserted; the Charrl are nearer to extinction than they’d realised. The larder is next to the Queen’s chambers, where Ace catches a glimpse of Muldwych and Ch’tizz conferring near the TARDIS shell as a group of Chronomancers use their mental powers to stabilise the rift through time and space. Before Ace can investigate, Seeba bursts into the larder to rescue Chel, thus attracting the attention of warrior Charrl who have no other thought but to protect the Hive’s larvae. The rescue party escapes with Chel into a disused tunnel, which leads in turn to an even older structure -- with writing on the walls which identifies it as a service corridor for the Channel Tunnel. Antýkhon is Earth, in the distant future.

While Ace tries to assimilate this discovery, she is contacted by a young Charrl named Isk, who is sickened by the blood shed in the Charrl’s struggle for survival and wants Ace to find some other way to help them. Ace agrees to meet Ch’tizz and Muldwych, who explain that some of the Charrl have passed through the Divide to dissect human women on the other side and determine their suitability as hosts for Charrl eggs. Since the Charrl cannot pass through the unstable Divide themselves, their only hope is to use the brief time they have to implant their eggs in hosts who will be consumed when the eggs hatch and the larvae eat their way out. Ace, however, has a better suggestion; although the dying Charrl are unable to pass through the Great Divide, healthy humanoids can still survive the journey. She therefore agrees to travel through the Divide herself, make contact with one of the alien civilisations monitoring the Earth in that time period, and thus get help for the Charrl. As a gesture of trust, she agrees to use the TARDIS’ Time Vector Generator to stabilise the Divide once she reaches the other side, and Ch’tizz agrees not to let her people pass through the stable Divide until Ace returns with help. Ace remains suspicious of Mulwdych, however, certain that his motives are not entirely altruistic.

Ace, Seeba and Korin pass through the Great Divide and materialise in London’s East End, where Constable Hawkins arrives in response to an anonymous phone call just in time for Ace to knock him out and steal his wallet. Inside, she finds the Doctor’s business card, and decides to go to the given address while Seeba and Korin search for the Charrl who have already passed through the Divide. Ace still isn’t sure how much of this the Doctor has planned, and therefore breaks into the house on Dean Street to search for the Time Vector Generator. When Benny arrives and surprises her, Ace accidentally knocks her out before realising who has just crept up behind her. Neither woman is sure how much the Doctor has told the other, and thus neither trusts the other completely. Benny is starting to feel feverish, and after they compare stories Ace slips Benny some knockout pills and goes to her bank to steal the TVG. When she returns, she meets Charlie and Popov, who have come to collect Benny for a Charrl hunt -- just as Seeba and Korin return, claiming to have found the dead bodies of the Charrl in a nearby warehouse. Ace goes to examine the bodies, but can learn nothing from them and has no way of knowing what women they have attacked. But when Popov tells Ace about the attack on Benny, Ace realises too late that Benny has been infected.

Benny wakes and stumbles out of the house, taking the TVG with her, and Ace catches up with her too late; as Khan watches from the bank of the Thames, Benny reinserts the TVG and restores the TARDIS to life. Khan absorbs the energy release into his own body and transfers his physical being into the TARDIS itself, possessing its structure. The energy release also cures Benny of her infection, and Ace gets her into the TARDIS before it dematerialises. The TARDIS is struggling to expel the intruder from its systems, and Benny, blaming herself for the ship’s predicament, dons a virtual reality helmet to do battle with Khan in the ship’s dataspace. There, she sees the Doctor as a puppet master using his companions for unthinkable purposes, and is unsure whether the images came from her mind or Khan’s. She is unable to defeat Khan, but learns that he was born in Scotland in the 13th century; as a lad he struck a deal with Ch’tizz, and has been seeking the TARDIS his entire life, not just to help the Charrl cross the Great Divide but to ensure his own immortality. Benny emerges from the datascape convinced that the monomaniacal Khan must be stopped, as he only cares about his own survival. She and Ace thus pilot the TARDIS to Antýkhon, where Khan senses the presence of the other half-TARDIS shell and tries to seize control of it as well. As Ace and Benny watch, the TARDIS takes advantage of Khan’s divided attention, expels him from itself into the half-TARDIS shell and then Time Rams it. The shell is expelled from the Time Vortex and explodes over Siberia in 1908, opening the Great Divide.

Benny and Ace then return to London, only to find that Ch’tizz has gone back on her word and allowed the Charrl to begin migrating through the Great Divide. Ace and Benny try to convince her to live peacefully amongst the humans, but unfortunately Popov arrives with the police, and a pitched battle breaks out. Muldwych, who was just trying to escape his own exile on Antýkhon all along, is horrified to learn that Ch’tizz intends to wipe out the human race to ensure her people’s survival. He thus threatens to use the TARDIS to close the Great Divide unless Ch’tizz halts the Migration; if she agrees, then he will use the ship to relocate the Divide’s opening to an alternate Earth in a timeline where human life never developed. Ch’tizz agrees to his terms, but after the last of the Charrl have passed through the Divide, Muldwych admits to Ace and Benny that he lied; in fact, he’s transported them to a sealed-off interior dimension in the TARDIS itself, where they will remain until he can find a new world for them to settle on. He then prepares to take the TARDIS away from Earth, claiming that he has a right to it after what he has done -- but the TARDIS rejects him as an intruder and expels him back to Antýkhon.

The Doctor enters the console room, brushing ice chips from his shoulders and claiming to have been in his room all along. Ace and Benny are understandably upset, but he points out that he can’t be everywhere at once -- and although he provides all the help he can, sometimes other people have to save the Universe themselves. Later, the Doctor visits Muldwych on Antýkhon, to ensure that the chastened exile understands that he will have to find some other means of escape. Ace has already guessed the real connection between the Doctor and Muldwych, but the Doctor will not confirm or deny her suspicions…