Something has gone terribly wrong with history. Following the Siberian incident, separate timelines have begun to overlap, and the Doctor has already had to deal with Sabbath’s attempt to seize control of infinity and extra-dimensional invaders in an alternate Edinburgh and Bristol. But the latest crisis is the worst of them all; humanity has discovered time travel in the early 21st century, and tourists are now visiting different eras of Earth history -- and taking their own culture with them. Luxury resort hotels have been built in Ancient Egypt and the American West, and history is being reshaped into a palatable holiday experience. The Doctor sends Anji and Fitz in to infiltrate Good Times, Inc., while he works on a plan to put things right. But shortly after they get themselves hired as tour guides, Anji unexpectedly contacts Fitz in the Wild West hotel and takes him back to 2003 with little explanation. A lot has happened to her since he last saw her that morning...

Jack Kowaczski, a bright American teenager from Jumpsville, Ohio, has just invented the world’s first time machine in his garage. The family’s Martian servant, Sio’phut, advises caution, but Jack is excited by his achievement and eagerly anticipates the adventure of time travel. He decides to travel back 150 years to see the Indians, but when he begins to travel through Time his time machine nearly collides with other machines in the vortex. He arrives safely in the past, but the valves on his machine have burned out -- and much to his surprise, he’s landed near a nightclub where Indian warriors dance and serve drinks to tourists from the future. Jack is spotted and questioned by Lieutenant Grania Flynn and Sergeant Jim Lamarra of the Time Police, who act as though he shouldn’t be there and whose version of history is different from anything Jack knows. Jack is willing to apologise if he’s done something wrong, but only one version of history can survive -- and Flynn and Lamarra take him out into the wilderness and shoot him in the head, killing him.

In another version of history, Jack Kowaczski has invented the world’s first time machine, and despite his Martian servant Sio’phut’s advice, he decides to test it by travelling back 1,000 years in time, innocently hoping to warn the Indians or the Martians about the white men who will invade and destroy their cultures in the future. But instead, his time machine collides with something else as it travels through Time, and ends up in a coffee plantation thousands of years in the past where ape-men have been put to work picking beans. So has a man who calls himself Ak, and when Ak learns that Jack has a time machine, he promptly steals it. When Jack tries to stop him he ends up dead, killed either by the force of the machine’s sudden departure or by Ak himself, who won’t let anyone prevent his escape.

And there are many, many other versions of Jack Kowaczski out there...

One version of Jack is rescued from Flynn and Lamarra by Fitz -- a Fitz who never received the visit from Anji and is still working as a tour guide in the West. Flynn and Lamarra believe Fitz to be a legitimate employee of Good Times from the “correct” version of history, and they reluctantly release Jack into his custody. Shaken by his narrow escape, Jack is stunned when Fitz explains that history is collapsing around their ears thanks to Good Times. The Doctor plans to arrange a conference between the leaders of the historical eras where Good Times has established resorts, and convince them to reject the time travellers. But history may be in even worse shape than they thought; when they return to town, they run into Fitz’s friend Anji, who doesn’t appear to recognise him. Fitz is shaken by this encounter, and when the mysterious Sabbath arrives with a newspaper article claiming that the Doctor was assassinated after taking the place of the murdered Pharaoh Cheops, Fitz doesn’t know what to think. Sabbath insists that the situation is desperate and that Fitz and Jack must help him to put things right, and Jack reluctantly accompanies Sabbath and Fitz, unsure whether to trust either of them.

In another version of history, a village of hunter-gatherers is attacked by the mechanical Others, and the only survivor is a young woman named Iyeeye, who was out in the fields at the time. Iyeeye flees to a circle of Stones where she can work magic which enables her to look into other times and other worlds. This time, instead of just looking, she lets the Time Magic sweep her away into one of these other worlds. There, she encounters two humans who appear to be working for the Others -- or so she believes when they try to lead her to a squat mechanical object on wheels. Fleeing from them, she finds her way to a tall blue Stone which seems more alive than the others she knows, and here, she meets a woman named Anji who appears to speak her language.

Anji soon realises that Iyeeye doesn’t belong here, and after assuring the skittish woman that the squat, Other-like machines are in fact vehicles called “cars,” she takes Iyeeye into town to meet Fitz -- or at least, a version of Fitz which is still here, along with Jack. Anji is disturbed by Iyeeye’s claim to come from a world where robots apparently harvest people for food and by her apparent ability to travel through Time simply by wishing it near the Stones. Anji thus decides to examine the Stones herself, and after conferring with Fitz she takes Jack with her in order to keep him safe from the Time Police. On the way to the Stones, she stops off at the TARDIS to update the Doctor, but there’s no sign of him. Frustrated, she and Jack accompany Iyeeye to the Stones, and once they get a good look at them, it’s clear that they are all fossilised copies of the TARDIS.

Out of her depth, Anji returns to her own TARDIS and tries to contact the Doctor once again, but there’s still no sign of him. Anji decides to fetch Fitz, and takes Jack with her but leaves Iyeeye to wait for the Doctor. Iyeeye instead catches another woman sneaking around the interior of the TARDIS; the stranger seems mischievous and evasive, and Iyeeye, fearing that the woman is trying to trick her, flees from the TARDIS only to find that it’s somehow become part of the circle of Stones. Panicking, she flees into the wilderness, but sees Fitz and Jack in the custody of the Time Police. The Time Police are taking their prisoners to the Stones, and Iyeeye follows them, hoping for the opportunity to rescue Fitz and Jack.

Anji and Jack return to Jumpsville for Fitz, only to find a mob of frightened tourists milling about the hotel. It seems that another version of Jack arrived in town, and Fitz was arrested for trying to help him. Anji and her version of Jack barely get away from the frightened mob of tourists, who aren’t sure what’s going on but are aware that it’s dangerous for people from alternate timelines to exist. Anji and Jack flee back to the Stones, but hear gunshots and find Fitz and the other Jack lying dead on the ground. Before they can react, the Time Police ambush them, and they flee for the TARDIS -- but will they make it in time?

One version of Fitz is dead, but not the same one who left Jumpsville in the company of Jack and Sabbath. The Jonah is floating on a river which wasn’t there that morning; history is changing so far back in the past that geography is changing in the present. Sabbath insists that this is the Doctor’s fault, as his attempts to fix history resulted in the human race discovering time travel before they were able to handle the technology, thus creating a series of paradoxes which threaten to tear the fabric of reality apart. Fitz still doesn’t believe that Sabbath can be trusted, but Anji’s rejection has shaken him badly and he doesn’t know what else to do.

Sabbath transports Jack and Fitz to Ancient Egypt, where they are greeted by Nubian soldiers and taken to the home of Lord Akhenaton. Strange things have been happening in Egypt, and the Pharaoh apparently blames both Akhenaton and his late father’s wife, a dark-skinned witch. Once Akhenaton is sure that the newcomers aren’t working for Cheops, he begins to speak modern American English, and identifies himself as another version of Jack Kowaczski. He claims that he was stranded in Egypt when his time machine broke down, and that he’s used his knowledge of future technology to get by; however, Jack can’t believe that this man is another version of him, and notes that some of Akhenaton’s language and attitudes belie his claim to be from the future. Sabbath takes Akhenaton aside to speak with him privately, but returns alone, claiming to have killed Akhenaton in self-defence. Jack concludes that Akhenaton was an Egyptian who met and killed another version of Jack Kowaczski and then tried to profit from his knowledge; if this is the case, it explains why he would have attacked any other time-travellers. But when they return to the Jonah, Sabbath tells the waiting guards that “it is done,” implying that he killed Akhenaton on Cheops’ behalf and knew what he was doing after all.

The late Pharaoh’s wife exists in a zone of temporal stability 300 miles inland, and Sabbath intends to visit her and find out how this is possible. Cheops agrees to escort them to the oasis, and on the long march they encounter “time ghosts,” images of another history which is beginning to overlap with this one -- a history in which Good Times, Inc. has built a resort in Ancient Egypt. Fitz and Jack are then attacked by Akhenaton, whom Fitz kills in self-defence -- and Sabbath warns them that there may be even more versions of Akhenaton out there. Now that there are no elementals to enforce the Laws of Time, there’s nothing to prevent a time traveller from changing history and thus creating another version of himself. Jack finally understands where the other versions of himself are coming from, and realises just how high the stakes are; there is a finite amount of energy in the Universe, and as more and more histories spring into existence, the available energy will be spread more and more thinly amongst them until nothing exists anywhere anymore.

As Fitz and Jack try to deal with these revelations, they are contacted by a Nubian guard who used to work for Cheops’ father and believes that the witch is more trustworthy than Sabbath. He directs them to the oasis, and Fitz and Jack desert the army and reach the oasis first. To Fitz’s disappointment, the witch is not Anji, but a woman named Iyeeye whom he’s never met. Iyeeye, however, has met Fitz before -- or rather, she met another version of him, the one who was killed in the Stone circle. This version of Iyeeye used the Time Magic to rescue Anji from the Time Police, but they ended up stranded in Ancient Egypt. Iyeeye married the Pharaoh in order to survive, but Anji died of a fever some years ago. She left a diary for Fitz telling him that she’d worked out why the Doctor never came to rescue her; there must be other versions of herself and Fitz out there, and she’s been abandoned because the Doctor rescued another Anji and never learned that this version needed his help. The Anji who wrote the diary died bitter but resigned to the fact that she had to die so another version of herself could live.

The ambush at the Stones has several possible outcomes. In one version, Jack gets into the TARDIS just in time, but instead of the Doctor he meets the same enigmatic woman whom Iyeeye met earlier. The woman calls herself “TX”, short for “transmission cancelled,” and claims to be a stowaway; however, she doesn’t risk leaving the TARDIS any more, for fear that she’ll create a duplicate of herself and that she won’t be the one to survive when the timelines merge again. TX hides when the Doctor arrives in the console room, but Jack has heard enough and is on the verge of panic, knowing that there are uncountable versions of himself out there -- and that almost all of them will have to die. The Doctor manages to calm him down, but the TARDIS appears to be under serious strain as it too is being duplicated and stretched throughout the numerous alternate versions of history. The Doctor manages to communicate with one of his own alternates, and together they formulate a plan which they hope will put things to rights. But in order for it to work, one of them will have to die.

In another version of history, the Doctor emerges from the TARDIS too late to save Jack, and shows the Time Police a badge which convinces them to release Anji and Iyeeye into his custody. When they enter the TARDIS, however, the Doctor is surprised to find the console room empty -- because he’d let Jack in just before he emerged. This is why he’s been trying to stay uninvolved; now that he’s become a part of events, the interior of the TARDIS is no longer protected, and it too is being duplicated by the changes to history. The Doctor and Iyeeye discuss Iyeeye’s use of Time Magic, and the Doctor comes to some unpleasant conclusions. He gives Anji a set of instructions, and Anji, overwhelmed by the rush of events, agrees to carry them out despite knowing that they’re likely to result in her death. Iyeeye, meanwhile, will have to kill the Doctor.

Cheops’ army arrives at Iyeeye’s oasis, where he orders his men to kill the witch for creating the “time ghosts” -- unaware that it is her survival and her link to the Stones which has been maintaining the stability of his timeline. Fitz and Jack are unable to prevent her execution, and when she dies, reality changes around them as Cheops’ Egypt is replaced by a Good Times resort town. The TARDIS then arrives, but Fitz’s relief is short-lived, as it dematerialises again after dropping off Anji. In order to restore the balance of history, it seems that the Doctor is now willing to sacrifice anyone, even his friends. Cheops, bewildered by the changes he has unleashed, demands that one of the newcomers guide him through this new world -- and as Sabbath, Jack and Fitz have all betrayed or abandoned him in some way, he agrees to let Anji guide him.

When Sabbath protests, Cheops orders his men to kill him, but Sabbath vanishes into thin air before they can do so. Fitz and Jack don’t have that ability, and must remain at the oasis as hostages to ensure Anji’s good behaviour. If Cheops doesn’t return by sunset, his men have orders to kill both Fitz and Jack. Unfortunately, Anji has instructions which she must carry out despite knowing this will result in their deaths. She thus leads Cheops and his retinue into the resort town, where Cheops naturally expects to receive the respect due a living god-king but instead gets tourists gaping at him and taking photographs. When he spots a building with a neon sign blazing the name “Cheops’ Palace,” he walks straight in only to see another man on the throne. Enraged, he stabs the usurper to death without realising that he’s just killed another version of himself, a Pharaoh Cheops who struck a deal with Good Times Inc. to turn his kingdom into a resort in exchange for the benefits of future technology.

Guards burst in and gun down Cheops and his retinue, but are too late to stop him from killing his other self. Anji survives, even though she was expecting to die, and the guards take her to a conference room where the Doctor and Sabbath are working together to put right the damage to history. Sabbath bribed the resort Pharaoh’s bodyguard, a young man named Akhenaton, to let the assassination take place, and he now intends that Akhenaton should take the dead Pharaoh’s place; however, the Doctor has other intentions, and in any case, Akhenaton is in no shape to take the throne. Many Egyptians have lost all respect for the Pharaoh after seeing the customs, beliefs and technology of the prosperous tourists from the future, and after seeing the Pharaoh killed by his other self, Akhenaton has lost his faith in everything, including reality itself. The Doctor decides to take Cheops’ place himself, and advises that the raving Akhenaton be exiled to one of the American coffee plantations.

The presence of two dead versions of Cheops would seem to prove that something is seriously wrong with history, but it isn’t enough. The head of Good Times Inc., Aaron Kowaczski, already knows that this kind of thing can happen, but still believes that the people in charge of the system aren’t affected by it. The Doctor must prove him wrong. He thus takes Anji to 2003, where he meets with Kowaczski, explains the situation to him, and offers to take the place of the murdered Pharaoh to prove his point. Kowaczski agrees to let him do so, and also agrees to let Anji remain on staff to investigate the Doctor’s allegations.

First, however, Sabbath arrives and claims that he needs Anji’s help -- and the situation is so dire that she and the Doctor have no choice but to work with him. Sabbath takes Anji back to the Old West resort where she and Fitz started working as tour guides, and tells her that she must pretend not to know Fitz in order to confuse him so Sabbath can convince him to travel to Iyeeye’s oasis. Sabbath has not in fact been there yet, but by taking Fitz and Jack there as Anji has already seen him do, he will create a thread of coherent causality which might be all that’s holding this reality together. Anji thus reluctantly pretends not to know Fitz when he greets her, and then travels back in time one day, grabs an earlier version of Fitz before he meets Jack, and takes him back to 2003 with her. Now, one version of Fitz will be killed at the Stones; one version will leave with Sabbath before that happens, but will presumably be killed at the oasis when Cheops fails to return; but the version who’s returned to 2003 with Anji has a chance to survive.

One version of the Doctor drops off Iyeeye in Cheops’ palace, where she assassinates the other Doctor, who has taken the place of the Pharaoh. It may even be the same Doctor; she doesn’t know any more. She escapes before the guards can arrest or kill her, and Sabbath transports her to safety -- or so he claims. Too late, Iyeeye realises that he’s delivering her to the robotic Others who hunted and harvested her people, or rather to the beings which control them.

Cheops fails to return to the oasis by sunset, and the guards therefore prepare to kill Fitz and Jack -- but before they can do so, an alien spaceship appears, and robots descend and begin to kill the guards. Iyeeye also descends from the spaceship, but it’s not the same Iyeeye that Fitz and Jack knew -- this one is dressed in silver and is armed with futuristic weaponry. She is the Iyeeye who assassinated the Doctor and was then “betrayed” by Sabbath, and she’s spent the last three years in the company of the beings who created the Others.

The Doctor’s assassination succeeded because his bodyguard allowed it -- his bodyguard being Akhenaton, a version who rejected exile to the coffee plantations in exchange for his help in arranging the Doctor’s death. Akhenaton is imprisoned for his role in the assassination, but is rescued by a surviving Doctor, who needs help to find his alternate self’s body. When the Doctor emerges from the cells, the guards and common people prostrate themselves before him, believing the Pharaoh has returned from the dead -- but the Time Police aren’t as credulous, and just as the Doctor finds his other self’s body they surround him, threatening to kill him if he’s from a history other than their own. The Doctor escapes using a device the dead Doctor had reserved in case he changed his mind at the last moment, and takes the body back to 2003, where he e-mails Anji and tells her to contact Aaron and arrange a board meeting.

Anji and Fitz have been in 2003 for six weeks, but the world has been changing around them, and the changes are accelerating. Only they and Aaron Kowaczski remain stable; the phone book and political boundaries between countries are changing, their co-workers are never the same from one day to the next, and now even the planet’s geography is changing. Aaron is unaware of the changes, but when the Doctor arrives with his own dead body, Aaron is forced to acknowledge that he may be wrong about the nature of time travel. He founded Good Times to regulate time travel after his son Jack was killed, but now the Doctor has proven that even the people Aaron thought were in control are affected by the paradoxes they’re creating.

Aaron calls the board together to discuss the situation, but the members of the board, the city landscape and the architecture of the boardroom change as they speak. Aaron is unaware of the changes as they occur, but Fitz is recording the meeting on a video camera, and when the Doctor rewinds the tape to show Aaron talking to a woman who no longer existed in the first place, Aaron finally understands that things are out of control and agrees to shut Good Times down. Either the decision comes too late or it’s this very act which destabilises the reality of Good Times Inc., and Aaron himself disappears into the ensuing changes. The Doctor, Fitz and Anji flee through a building which is not the same from one second to the next, and reach the safety of the TARDIS just as reality collapses completely outside.

There is only one stable point left in all of time and space -- Sabbath, who is now the only unique individual in the Universe, perhaps because of the help of his mysterious allies. The Doctor tracks him down at Iyeeye’s oasis and materialises there, but when he, Fitz and Anji emerge from the TARDIS, they find that they’ve already arrived there -- several times over. Since the oasis is the only stable point in time and space, every single surviving version of the Doctor from all of the uncountable versions of reality is making for it. Thousands upon thousands of TARDISes are materialising, bringing thousands and thousands of Doctors, Fitzes, and Anjis -- and only one of each can survive.

In the ensuing chaos, several versions of Anji sacrifice themselves so one of the others may live, and the Fitz who first arrived at the oasis with Jack and Sabbath falls to his death while trying to climb into the Others’ spacecraft -- which is no longer able to maintain its balance as TARDISes pile up on its hull. At least one Doctor, one Anji and one Fitz make it aboard the Others’ spacecraft with Sabbath, Jack and the Iyeeye who came here with the Others, but in order to save the Universe they must break all of the millions upon millions of causal links which led up to this disaster.

Before they go, however, they receive a fuller explanation from one of the Others’ masters -- a Martian named Man’ofret, who explains that this was all caused by Jack Kowaczski and his time machine. Many millions of Jacks travelled back in time to visit ancient Mars, only to arrive on a world incapable of supporting life -- but as Mars became littered with corpses, the bodies began to decay and the bacteria within them evolved, transforming the planet’s atmosphere and surface and eventually resulting in the birth of the Martian race which Jack knew. And then other versions of Jack kept arriving from a future in which the Martians had been enslaved by the human race... and so the Martians invaded Earth first and turned it into Iyeeye’s world, allowing the best and brightest of humanity to join their culture and using robots to cull the rest before they posed a threat. However, the Martians have always known that their history was based upon a paradox, and now that the time has come, they accept that the Doctor must put an end to it to save the Universe.

The Doctor, Sabbath, Anji, Fitz, Iyeeye, and two versions of Jack depart in a TARDIS belonging to a Doctor who was unable to save his friends and thus arrived here alone. As they depart, the Others’ spaceship explodes, presumably unable to cope with the strain of being weighed down by so many TARDISes. Now, the Doctor and Sabbath must break the links which led up to this disaster by going back and preventing the first event which started the chain.

Jack Kowaczski invents the time machine and travels back in time 50 years, but the Time Police are waiting for him. Congress passed a statute of time travel prevention in 1943, and Jack is thus sentenced to death and gunned down on the spot. However, he left the blueprints of the time machine behind him, and his father Aaron finds them and realises what’s happened to his son. Aaron gets an engineer friend to build the time machine in the hope of finding his son, but the Time Police arrive and shoot them both before they can activate it. But in another version of history, Aaron manages to activate the time machine first and escape from the Time Police. Sabbath tracks down this version of Aaron and shoots him before the Doctor can stop him, but it’s clear that there are still too many alternatives to stamp out one by one. They will have to dispose of Jack before he ever conceives of the notion of time travel -- but the Doctor refuses to let Sabbath kill him. Instead, he kidnaps Jack while he’s still a baby and takes him back to the Good Times resort in Ancient Egypt, where he leaves him to be raised by a native woman -- a woman who can’t read the note left with the baby and who thus decides to name her newly adopted son Akhenaton.