Travel between the colonies of Earth’s solar system has never been easier, thanks to a subspace mass transit system which pokes holes through interstitial reality. Now, on the anniversary of Earth’s victory over the Ice Warriors, the STS is about to initiate the Star Tunnel to Acturus and open up instant travel to other star systems. But there have been a number of unexplained power losses over the past few days, and even the floozies, the STS maintenance team, can’t find the cause. Nevertheless, the controlled shutdown of the network begins, diverting power for the Stunnel initiation -- although there is something odd about the texture of the carrier wave.

Many years ago, a young soldier named Alistair Gordon Lethbridge-Stewart was briefly stationed in Africa, where he met a strong-willed and intelligent native woman… and at the time of the Stunnel initiation, his descendant Kadiatu is a student at Lunarversity. She is desperately short of money with half the term left to go, and is forced to take a job delivering a package to the floozie Old Sam -- a veteran of the Mars conflict who can no longer function without the combat drugs once used to augment him for battle. Kadiatu joins the floozies as they ride the transit lines to celebrate Constitution Day, and makes love to the young Blondie -- but when she wakes the next morning outside Peking, Blondie is gone, and the moneypen containing Old Sam’s payment has been stolen. Broke and stranded, Kadiatu tries to crash the transit system to reach the only person who can help her, but she is spotted and pursued by a ticket inspector.

The Stunnel initiation begins on schedule, but in the middle of the President’s speech something from the other side of the carrier wave explodes through the gateway and roars down the Central Line, shredding everything in its path. The TARDIS materialises at King’s Cross station just as Kadiatu arrives, and the Doctor emerges moments before the invader passes through. He pulls Kadiatu out of harm’s way, but the ticket inspector is killed, and the TARDIS -- and Benny -- are catapulted down to the very end of the line. The Central Line is shut down for emergency repairs and investigation, and the Doctor, unable to follow his TARDIS, decides to accompany Kadiatu while he works out what to do next. First, Kadiatu visits an old family friend, the blind war veteran Francine, who agrees to set the Veteran’s Association on Blondie -- and tells Kadiatu that her new friend has two hearts. Kadiatu takes the Doctor to a cafe at Piarievs, where he gets drunk and passes out celebrating the Universe’s 13500020012th birthday. She knows who the Doctor really is, and once again he has arrived on Earth during a crisis, as rumours about the incident at the Acturus terminal begin to spread through the system.

Benny arrives in Lowell Depot, the ghetto at the end of the line, where she is pulled off the streets by two hookers, Zamina and Roberta. Blondie is originally from the Stop, and Roberta has never forgiven him for getting out in one piece; it was she who stole Kadiatu’s moneypen, seizing the opportunity when she saw Blondie and Kadiatu making love. Benny convinces them to take her to a local gang, and convinces the gang leader that she can help him gain power and take control of the entire Stop. Zamina realises that Benny has her own agenda, but is unable to intervene as Benny’s manipulation causes all of the pent-up frustration and anger in the Stop to explode into violence. The Stop becomes an urban war zone, and Roberta is killed before the military arrives to quell the uprising and evacuate the survivors.

The Doctor awakens in Kadiatu’s room on Lunarversity, and as he studies the sleeping Kadiatu he realises that she has been genetically engineered. When he hacks into her computer, he finds that she has pieced together her family stories and historical records to work out who he is -- and that she has nearly solved the theoretical equations that will enable her to build a time machine. Curious, he decides to let her continue to see what will happen. When she awakens, he accompanies her to the drug lord whose money she lost, to find that he is under arrest. The Doctor bluffs his way in and convinces the arresting officer that he’s from a higher government authority, and she agrees to release the dealer so the Doctor’s organisation can keep track of his movements. Having solved Kadiatu’s problem for her, the Doctor then asks her to help him rescue Benny from the Stop.

Something shaped like a train but made out of folded segments of reality is roaming the transit tunnels, capturing lone passengers and “freesurfers” who ride the tunnels on reality surfboards, and transforming them into mutant warriors and intelligence operatives. The floozies are sent into the tunnels to investigate reports of “unspecified incidents” and barely escape with their lives from a party of mutants. As they recover back at the STS base, Francine contacts Old Sam about Blondie, but the young floozie manages to convince them both that he knows nothing about Kadiatu’s moneypen. The STS surveillance system spots Kadiatu and the Doctor heading for the Stop, an urban riot zone and the heart of the “incidents”, and Old Sam and Blondie set off to investigate and to rescue Kadiatu if necessary.

The Doctor and Kadiatu stow away on a service train taking supplies to the relief workers at the Stop. This is the end of the line, and the TARDIS has entered the final station with such force that it has been embedded in the concrete -- with its door facing the wrong way. As the Doctor puzzles over this fresh problem, Benny arrives and tries to kill him; the intelligence which has possessed her doesn’t seem to regard the Doctor as complex enough to be dangerous, but Benny knows that he poses a real threat to the plan. Old Sam and Blondie arrive just in time to save him, and Benny flees as the mutant warriors cover her retreat. She and Zamina join the rest of the evacuees and are shipped off to the refugee relocation centre on Mars… which was Benny’s plan all along. Meanwhile, Kadiatu, fighting for the first time in her life, finds that she can instinctively locate her opponents’ weaknesses and punch hard enough to kill. She does not yet know the truth about her birth. Years ago, a mysterious hacker told Francine that the company Imogen was manufacturing genetically enhanced super-soldiers, and she sent a fellow war veteran to destroy the company and shut down the monstrous project. But although he destroyed all of the project records, he was unable to murder the baby he found in their R&D creche, and despite the risk, he adopted it… and named it Kadiatu.

The Doctor takes Kadiatu and Blondie to his house on Allen Road, where he makes pasta while the humans make love. He considers the situation and deduces that the interstitial tunnel system has grown complex enough to resemble a neural network, which would make the invader analogous to a computer virus -- and when he learns that the power failures began before the invasion, he realises that the network has already evolved its own intelligence. He builds a machine from spare parts with which to hack into the network and contact the Transit intelligence, which borrows the form of virtual TV host Yak Harris to speak with him. Yak confirms that the system was infected while its defenses were down, by a form of viral cancer from another dimension. The Doctor thus contacts the surviving STS executives, explains the situation to them and offers his expert assistance. It’s going to be needed, and soon, for the floozies have discovered that something on the other end of the dimensional breach is channeling energy into the initiation grid and preparing to open the Stunnel again…

Benny and Zamina are placed with foster boarders on Mars, but Benny doesn’t intend to stay with them for long; now that she’s out of the ghetto and on Mars, she can access STS control and set the next phase in motion. The virus’ influence over Benny weakens with her distance from the transit system, however, and she manages to resist it long enough to send Zamina to the Doctor with a warning. The Doctor takes Kadiatu with him to rescue Benny, only to find that she has killed her foster family and is fleeing out of the terraformed area of Mars, killing everyone she encounters on the way. They pursue her to a dormant Ice Warrior nest, where Kadiatu, realising that Benny has been possessed by the virus’ core programme, shoots and kills her before the Doctor can intervene. Or so she thinks until the Doctor examines the body and discovers that this isn’t the real Benny -- one of the virus’ victims was transformed into a decoy and sent to distract them, while the real Benny carries out the next stage of the plan elsewhere. The Doctor and Kadiatu return to the surface to wait for Francine to pick them up, realising that this disturbance will have caused the Ice Warriors in this nest to begin waking.

While waiting for Francine to pick them up, Kadiatu tells the Doctor about her offshoot of the Lethbridge-Stewart clan, and her dreams of an old woman falling into a pit. Francine pilots them back to Olympus Mons, unaware that a forgotten software defense system left over from the war has automatically been reactivated by the current crisis. When they fail to transmit the proper clearance codes, the security systems shoot them down before anybody realises what is happening. Nevertheless, Francine manages to land safely, and the Doctor is embarrassed when a member of the rescue party identifies him as Shango, the lightning god. The worship of Shango is indeed derived from a visit he made to Earth centuries ago. He’s getting far too well known here, and Kadiatu is dreaming of the Pythia of Gallifrey and her curse. Perhaps Kadiatu is a natural response to the Doctor’s presence on Earth -- the planet has evolved her in response to his interference in its history.

Benny is spotted heading for the STS reactors, and although the Doctor and Kadiatu give chase they find that once again they’ve been distracted by a decoy. The decoy overloads the reactors and floods the Stunnel initiation grid; the breach will reopen before the human forces are ready for it. The Doctor sends a set of the floozies’ maintenance drones to Lowell Depot, to build a machine connected to the TARDIS, and freesurfs through the tunnels to confront the invader in person at the Stunnel station. On the way, he picks up a telepathic hitch-hiker, which enters his mind while he’s passing through one of the reality junctions between stations. Meanwhile, the floozies and soldiers waiting at the Stunnel terminal discover too late that the Kwik-Kurry franchise operator who has supplied them with food is Benny in disguise, and she’s smuggled a party of mutant warriors in with her. Blondie is killed in the fighting. The Doctor arrives just as the Stunnel opens up again, and an invisible intelligence emerges and possesses Benny. The virus they have been fighting was only an agent laying the groundwork for the arrival of the real invader. It has no name, and the Doctor therefore decides to call it Fred. But before Fred can do anything in its new domain, the machine at Lowell Depot fires a burst of artron energy out of the TARDIS, through the tunnels and into the Doctor, who channels it through Fred and forces it back through the gateway into its own dimension. It takes Benny with it, however, and the Doctor and Kadiatu follow as the Stunnel begins to collapse.

In Fred’s home dimension, the Doctor creates an analogue of reality enabling him to function. The burst of artron energy takes on the form of two cats, one silver and one green; the green one bites the Doctor’s finger when he reaches out to it. The Doctor then attends the ruler of this world to negotiate Benny’s release. As it happens, the ruler of this world is Fred; unlike its virus, it recognises the Doctor’s potential, and it kidnapped Benny to lure the Doctor here, where it could defeat him on its home turf. But as Fred tries to absorb the Doctor into itself and acquire his knowledge, Kadiatu arrives in the form of a fierce black leopard -- and while Fred is distracted, the Doctor pushes his hitch-hiker out of his mind and into Benny’s, forcing Fred out. The leopard eats Fred, and the hitch-hiker vacates Benny’s mind and resolves itself as the Transit intelligence in the shape of Yak Harris. Harris decides to remain in this dimension, where it can achieve its full potential, and the Doctor, Benny and Kadiatu return to their reality moments before the gateway collapses.

Before leaving, the Doctor visits the Stone Mountain archives where Earth’s history is stored. The software which runs the archive has evolved its own sentience, and the Doctor threatens to expose it to the paranoid human race unless it destroys all records of his existence on Earth. It does so, and in exchange, the Doctor offers it some useful advice on how to co-exist with humanity; it decides to begin by naming itself FLORANCE. The surviving floozies cut the TARDIS out of the rock at Lowell Depot, and the Doctor departs with Benny, who remains shaken by her experience and now understands that in evolutionary terms she is basically the equivalent of the Doctor’s favourite pet. Old Sam, a veteran of the war with the Ice Warriors, goes to the waking Ice Warrior nest and makes a symbolic gesture of peace. Kadiatu gets a job with STS, and thus gains access to the resources she needs to build her time machine -- but she then destroys her research and sets off after the Doctor alone. The human race is not ready for time travel, but at least one of them has stepped up to a new level of the game. But will she be the Doctor’s friend or his foe?