Due to the machinations of Sabbath and his mysterious allies, the multiverse is collapsing down into a single timeline. If the collapse is allowed to run on unchecked, all of time and space could be wiped out of existence. The Doctor, Fitz and Anji are lost amidst the shuffling realities, and they’ve recently learned that they have another companion -- con woman Beatrix “Trix” MacMillan, who slipped aboard the TARDIS in Siberia without their knowledge out of an interest in the opportunities afforded her by time travel. As if this wasn’t enough, in order to prevent a catastrophic time paradox, the Doctor must sell Fitz’s journal to a used bookshop in 1938 so his past self can purchase it -- but in order to accomplish this, he must first find the correct timeline.
To keep matters straight in his own mind, Fitz tries filming a documentary about the crisis, and though the Doctor is initially irritated by Fitz’s apparently flippant attitude he soon calms down and apologises -- and a comment from Anji about a pre-titles sequence inspires the Doctor to try a new approach. Perhaps he can slip back into their reality by going back to the Big Bang and trying to enter the Universe from the very beginning. Piloting the TARDIS through the primal forces of creation is extremely dangerous, however, and before doing so, the Doctor surreptitiously drugs his companions so they won’t know if anything goes wrong. It very nearly does, but just as the TARDIS is about to be torn apart, a young girl named Chloe arrives with her doll and her pet Jamais, an alien animal which exhales Time out over the TARDIS console, washing it millions of years forward into the future -- in the proper timeline at last. Chloe reveals that she’s been waiting for the Doctor, whose arrival was foretold in a book which she carries with her at all times -- and now that she’s saved him, he must do her a favour.
The Doctor therefore takes his companions to present-day England to save the life of Guy Adams, a junior civil servant in the Department of Environment, Food and Rural Affairs. While Guy’s supervisor Mike was on holiday, Guy tidied up the paperwork on his desk, but Mike is strangely angered by Guy’s presumption -- and suddenly Guy finds that everybody he knows is trying to kill him. The Doctor and his companions intervene to save Guy’s life, but Guy’s six-year-old nephew Pete is horribly burned when he douses himself with petrol and sets himself alight while hugging his uncle. Anji arranges for Pete to be sent to the hospital and takes Guy to her city flat to hide out from his friends and family.
The Doctor gives Guy a lotion which heals his burns, but can find nothing extraordinary about Guy apart from a few minor quirks in his DNA. As Guy rests in Anji’s guest room, trying to come to terms with what’s happened to him, Anji notices that the Doctor still hasn’t taken the journal back to 1938, which he needs to do in order to stabilise this history as the primary timeline. However, the Doctor is concerned that this may be just what Sabbath’s masters want to happen, and he’s not sure whether doing their work is such a good idea. In any case, he’s still unsure why some alien force seems to be trying to kill Guy by magnifying his friends and family members’ minor irritations and grudges to such an extent that they’re willing to murder.
Chloe visits the Doctor once again, and again he agrees to help her by sending Fitz and Trix undercover to investigate the activities of a man named Daniel Basalt. Posing as the nouveau riche Ralf and Susan Canonshire, Fitz and Trix make contact with Daniel and pay a fortune in diamonds in exchange for being allowed to commit a consequence-free murder. Fitz is unnerved by the thoroughness with which Trix vanishes into her role as Susan, and by the ease with which they’ve purchased the right to murder an Italian immigrant named Pietro Nencini. While Trix investigates Nencini, Fitz follows Basalt to Bournemouth, where he sees the man brutally murder a 50-year-old woman in a wheelchair. Basalt and his cohorts leave the house with suspiciously-shaped garbage bags and plenty of cleaning equipment -- and Fitz then sees the murdered woman through the window, standing on her own two feet. He speaks with her briefly, posing as her neighbour, and leaves convinced that though they are apparently identical, the woman he saw killed is not the same woman he spoke to -- and that the woman he spoke to has no idea who her real neighbours are and has never used a wheelchair in her life.
Chloe has been told off for talking to the Doctor out of turn. Upset, she takes Jamais and her dolly back to see the beginning of the Universe again; however, the jealous Jamais is resentful of the attention Chloe shows to her dolly. He has, on several occasions, attempted to bite and mar the doll. Displeased with his behaviour, Chloe returns to her home, to a room filled with diamonds which represent all of the souls which the Timeless organisation has saved -- such as the 50-ish Celia, who was crippled for life in the same accident which killed her husband, at least until Chloe and her guardian Erasmus came to offer her a better life. Recently, however, Chloe’s actions have been constrained by her book, which tells her the future but won’t let her read ahead to the end; when she tried, it twisted her eyes out of shape as a punishment.
Despite his concerns, the Doctor decides to return Fitz’s journal to 1938 and settle reality into place. He leaves Guy in Anji’s care, but Guy still doesn’t really grasp the reality of the situation and insists upon using the Doctor’s miracle burn cream on the injured Pete. Anji becomes irritated and attempts to kill Guy, and by the time she realises what she’s doing, he has fled in terror. Realising that he’s on his way to the hospital to help Pete, Anji follows him, but on the way she runs into Chloe, who tells her that Jamais is helping to protect Anji from the misty, wraith-like figures which have been driving people to kill Guy.
Unnerved -- especially by the fact that Chloe called her “Mum” -- Anji continues on to the hospital. There, Guy uses the burn cream on Pete but then must flee from a suspicious nurse. Outside, he runs into Mike, who claims that he’s followed Guy to ask him about the paperwork he sorted out. Mike then tries to kill Guy again, but Anji arrives and overpowers him, and she and Guy flee. Shaken and unsure what just happened, Mike is then contacted by Daniel Basalt, who accuses Mike of overreacting to Guy’s indiscretion and putting their scheme in jeopardy.
The Doctor returns to 1938 and sells Fitz’s journal to the used bookshop three days before his past self will purchase it, putting reality on track. As he returns to the TARDIS, however, he is assaulted by misty, wraith-like figures, and although he escapes into the TARDIS, it takes him to a beach in Newhaven instead of to Anji’s flat. Disoriented by the wraiths, the Doctor falls into the sea, but is saved from drowning by an American named Stacy Phillips. The Doctor recognises Stacy’s picture from Chloe’s book and follows her to her bed and breakfast, where she admits that she’s looking for evidence of murder. She is a criminal psychologist, and she’s being taunted by Daniel Basalt, who has provided her with incontrovertible evidence that he’s murdered several people -- who are nevertheless still alive. Determined to prove Basalt’s guilt, she’s come to Newhaven to find proof that he has been dumping his victims’ bodies in the sea as he claimed. The Doctor agrees to help her investigate.
Chloe remembers when things went wrong for her, in France in May 1830, when she saw a man named D’Amantine steal a pouch of diamonds and deliver them to his master, Sabbath. This wasn’t what Sabbath intended D’Amantine to do, but his associate Kalicum, who made the genetic alterations to D’Amantine’s ancestor, also planted this impulse, partly as a joke and partly as a test of the alterations he had conducted. Sabbath then spotted Chloe watching him and captured her, recognising her potential as a time-sensitive. When she touched him, she lost consciousness, overwhelmed by his sense of certainty -- and when she recovered, she found that although Jamais had stolen one of Sabbath’s diamonds, Sabbath had left her a book depicting the future, a book to which she has been bound ever since.
Guy finally accepts the danger he’s in when he calls his mother for help and she attacks him with a machete. He and Anji thus decide to investigate their only lead -- Mike, whose trigger for murder seemed to be the paperwork Guy sorted for him. They successfully break into Mike’s office, but find nothing extraordinary apart from an odd file folder listing cargo deliveries from Newhaven with no destination. Elsewhere, Fitz and Trix compare notes and determine that Pietro Nencini, a non-entity wasting his life away in a squalid little flat in England, is also a wealthy and happy art dealer living comfortably in Italy. They break into Nencini’s flat to take a blood sample for the Doctor to analyse, and the sleeping Nencini barely stirs as they do so, as if he’s too depressed to live.
The Doctor and Stacy visit the marina, reasoning that Basalt must be using a boat to dispose of his victims. They are unexpectedly aided when the Doctor’s vision blurs; some alien entities, presumably the wraiths, are trying to communicate with him psychically, but can’t interface properly with his senses. The mist directs the Doctor to a white van containing a casket bound with steel cables and full of air holes, as if it’s meant to imprison a living being. The mist also leads him to two thugs who are being paid by Basalt’s associate Chong to dispose of these “coffins” in the sea, no questions asked. Chong escapes with the van and the casket, and the Doctor, apparently back to square one, takes the surprised Stacy back to Anji’s flat in the TARDIS to compare notes with the others.
Guy recognises Stacy’s description of the casket from the van and reveals that it’s a coffin for burial at sea; the steel cables hold the lid shut underwater and the “air holes” enable the coffin to fill with water so it will sink rather than floating. This may explain why Mike is involved; Basalt is processing his victims’ burials through Mike’s department with the proper paperwork but false names, so if something goes wrong and a coffin resurfaces, the police won’t start asking the wrong kinds of questions. The Doctor decides to investigate Basalt further by going through Mike’s paperwork; Trix offers to go back undercover as Susan Canonshire to get close to Basalt, but the Doctor rejects this plan as too dangerous. Trix is peeved, realising that the Doctor only asked her to investigate Nencini in the first place as a test to see if she could be trusted.
Basalt himself is close to getting what he wants. He’s driven by a desire to control his life, and he takes what he wants from those weaker than himself, including a string of abused women. He has made a deal to kill twenty people who will never be missed, and has made a profit on the side by allowing others to do the actual deed in some cases. However, Chong informs him that something has gone wrong with the latest burial, and Basalt is forced to warn Erasmus and Chloe that someone is investigating the disposal of the bodies. Though disturbed by the nitty-gritty details of what Daniel does, they nevertheless agree to meet him at the warehouse the next day to discuss any necessary changes in operations.
Jamais is beginning to sicken, and Chloe fears that the wraith things are responsible -- and since Jamais’ homeworld no longer exists, neither she nor Erasmus have any way of helping him. Chloe feels events closing in on her, as if she’s being watched; for the first time, Erasmus has actually noticed her locket, a present from a Tsar’s daughter in which Chloe had placed the diamond which Jamais stole from Sabbath in 1830. Meanwhile, Daniel arrives at the warehouse to speak with Chong, only to be captured by Sabbath and his ape servants, who have come to shut down Timeless. Kalicum, apparently fascinated by the brutality of this era, drags Chong away to torture him to death while Sabbath holds Basalt at gunpoint, ordering him to put Chloe and Erasmus at their ease when they arrive so that Sabbath may capture them.
The Doctor and Anji visit Florence and take a blood sample from the wealthy Pietro Nencini, and analysis confirms that he and the man wasting his life away in London are the same person. The Doctor deduces that one of the Nencinis is from an alternate timeline, and suspects that Chloe knows more than she’s been saying. He suspects that Chloe and Jamais are survivors of a great disaster on a world with time-travel capabilities, or possibly from a world contaminated by the fallout of such a disaster. In any case, Chloe has the ability to cross between timelines at will, but recently her actions have been dictated by the book which she showed to the Doctor. The book told her that Guy Adams had to be kept alive -- but who wrote the book?
Searching for Basalt, Stacy tracks down one of his abused “girlfriends,” and is disgusted by the passive woman, feeling that she’s let herself become a victim. Meanwhile, Guy and Fitz look over Mike’s paperwork and realise that he’s amused himself while covering his tracks by twisting around the names of Daniel’s victims for the forms -- for example, changing the name of “Holly Fulbright” to “Ivy Black.” Trix phones up some of the offices on Mike’s list and locates one which recently delivered a bulk order of sea coffins to a warehouse just outside town. She, Fitz and Guy head for the warehouse to investigate, evading another wraith attack on the way, and leaving Stacy asleep back in Anji’s flat.
The TARDIS tracks down an energy signature from something similar to itself and materialises near the Timeless offices -- Erasmus’s time ship -- but when the Doctor and Anji investigate, they are assaulted by the wraiths. The Doctor tries to communicate with the wraiths, but they tell him more than he to handle, and when Jamais draws the Doctor and Anji to safety in the Timeless ship, the Doctor begs Chloe to kill him. Chloe allows him to faint, and when he wakes he’s forgotten much of what he learned -- as he had to, in order to survive -- but he knows enough to understand what Chloe has been doing.
According to Chloe, her world went rotten and had to be cut out of existence by “the Blessed Destroyer,” and ever since then the survivors have wandered eternity, having learned that they must participate in the universe rather than cutting themselves off from it. Chloe has thus been “saving” people from other timelines with Jamais’ help. A person’s soul is effectively the sum of their experiences, and since Jamais can biologically manipulate Time, he can move the essence of people’s lives out of their bodies in one timeline and into another. Whenever Chloe meets someone whose life has gone wrong, either due to a tragic accident or poor choices, she can transfer them to a better life; the two souls merge, but the leftover life must then be disposed of. This is where Basalt comes in, but Chloe, distressed by the evil glee with which he does the “cleaning up,” wants the Doctor to deal with him before she must reward him for his work by sending him to his own ideal timeline.
The Doctor and Anji are appalled by Chloe’s naive attitude towards what amounts to murder, and when Chloe admits that her book was forced upon her by Sabbath, the Doctor realises that by keeping Guy alive at her request he has somehow been serving Sabbath’s ends. When the Doctor’s attitude towards Chloe becomes threatening, Jamais expels him from the Timeless building, but the Doctor has learned enough to make him worried. The wraiths are a living part of the fabric of time and space, and they warned him that the universe has recently become imbued with some force which, though it only appeared recently, has somehow always been there. Jamais’ ability to travel back to the void before the beginning of Time must somehow be related to this threat, which is why the wraiths have been focussing on Chloe’s activities. Daniel Basalt has only ever been a sideshow; the real threat is Sabbath, whose plans may finally be nearing fruition.
Unable to locate Sabbath’s ship, the Jonah, the Doctor begins to slide into despair. He can no longer deny Anji’s suspicions that Chloe and Erasmus are of the Doctor’s own race, but he doesn’t regard himself as a survivor like them. And despite all of his efforts to champion life, he now feels as though he’s been used and manipulated into putting all of existence at risk. Anji forces him to snap out of his gloom, and the TARDIS then picks up a signal from a temporal bolt-hole, a small space cut off from the rest of time and space, presumably where Sabbath can store something which will be unaffected by anything in the exterior universe. Re-energised, the Doctor prepares to investigate.
Guy, Fitz and Trix arrive at the warehouse, and Trix, disguised as an old lady, goes on ahead to investigate. Inside, Basalt intends to take Chloe hostage when she arrives, guessing that Sabbath won’t want him to kill her; he doesn’t care what Sabbath does with Chloe, but intends to force her to send him to his ideal timeline before he loses contact with her. However, when Trix arrives unexpectedly, this throws off Basalt’s plans, and in the ensuing confusion, Chloe, Erasmus and Jamais arrive and are captured by Sabbath’s apes. Guy and Fitz attempt to rescue Trix, but Guy falls into a trance as soon as he gets near to Sabbath, who has also been waiting for him to arrive.
Basalt escapes with his life, but realises that he’s been played by Sabbath and will now never get to the ideal timeline which Chloe had promised him. Furious, he returns to the city to salvage what he can from the mess. At the warehouse, Kalicum takes Trix prisoner, presumably to satisfy his own sadistic desires, while Sabbath demands that Chloe give him the diamonds she keeps in her timeship to remind herself of the souls she’s saved. In the struggle, she’s lost her precious locket, and although Sabbath’s manner seems gentle he tells her that her people’s time has passed -- and that new masters will now arise to rule all of time and space.
Stacy wakes in Anji’s flat to find that the others have gone. Unwilling to be left out, she tracks down Nencini’s apartment to investigate on her own, but arrives just as Basalt finishes murdering Nencini. Before she can flee he attacks her, revealing that he’s been stalking her because she is one of Chloe’s “saved” souls. Before Basalt killed her other self, he kept her as one of his abused women; Chloe had promised to send him to a history where he and a meek, compliant Stacy could be together forever, but as he’s lost that chance he intends to take what he can from the real Stacy. At the last moment, Fitz bursts into the apartment, having hidden inside Basalt’s car during the confused fracas outside the warehouse. As Basalt fights Fitz off, the enraged Stacy smashes Basalt’s head in with a candlestick. The Doctor and Anji then arrive to collect Fitz, but Stacy has learned all she cares to handle, and remains with Basalt to wait for the paramedics while the Doctor, Anji and Fitz set off to rescue Guy and Trix.
The TARDIS materialises next to the Jonah, which is moored in the river behind Basalt’s warehouse. Fitz sets up his camcorder to play his “documentary” about the alternate timelines, distracting the ape guards while the Doctor and Anji slip aboard Sabbath’s ship. They locate a chamber in temporal stasis, isolated from the rest of the universe, which contains a canister made of the incredibly dense dwarfstar alloy -- and Guy and Trix, trapped in a cell of light.
Sabbath transmats Chloe’s diamonds into the stasis chamber and forces Erasmus to materialise his ship around the Jonah. However, it also materialises around the Doctor’s TARDIS, and the resulting interference prevents Erasmus from taking off again. Sabbath investigates, and catches the Doctor and Anji before they can release Trix or Guy. The Doctor demands an explanation, and Sabbath reveals that, centuries ago, Kalicum altered the genetic structure of a Frenchman named D’Amantine; now, 13 generations later, his descendant Guy has become the perfect host for a life essence which Kalicum has transferred into Chloe’s diamonds. Now that the glitches and discontinuities in the fabric of time and space have been smoothed out by the collapse of the multiverse, Sabbath intends to implant the diamonds into Guy’s body, place it in the dwarfstar canister and send it back to the void before the creation of the Universe; the alien essence within will then interact with the forces of the Big Bang, and permeate all of time and space.
Sabbath’s apes hear Trix imitating the Doctor’s voice in Fitz’s documentary and go berserk, and Fitz fires at them with his tranquilliser gun, misses at least once, and flees for his life. When he gets out of the Jonah, however, he finds himself inside the Timeless building. Erasmus, Chloe and Jamais are there, trapped within a metal net which constrains their ability to perceive and manipulate time. The wraiths return and try forcing Fitz to shoot and kill Jamais, but Jamais consumes the wraiths as they flock around him; however, their substance is toxic to him, and his efforts to protect Chloe and Anji are causing him to age unnaturally. Erasmus realises that his and Chloe’s good intentions have led the Universe to the point of catastrophe, and he shoots himself, unable to bear the guilt. Unable to free Chloe or Jamais, Fitz flees, hoping to find a weapon in Anji’s car, and reluctantly leaving Chloe alone with Jamais and her doll.
Sabbath agrees to let the Doctor depart with Trix, but Kalicum claims that he still needs her -- and Kalicum then pulls a gun on Sabbath, telling him that his usefulness is over. The Doctor refuses to move his TARDIS unless Kalicum releases his friends, but since Guy and Trix are vital to Kalicum’s plans, he only allows the Doctor to depart with Anji and Sabbath. In the TARDIS, Sabbath reveals that he was rescued from drowning during his initiation into the Service by a delegation of humans from the distant future, who showed him the horrors that lie beneath the surface of ordinary Time. Ever since, he has willingly helped them to eradicate those threats and smooth out the inconsistencies in history, all leading up to this moment, when the essence of humanity will be implanted in Guy and carried back to the Big Bang to imbue the entire fabric of the Universe and ensure humanity’s dominance over time and space. But now that Kalicum, the representative of his so-called allies, has turned upon him at the last moment, Sabbath is starting to suspect that those allies are not human after all.
The TARDIS dematerialises from Erasmus’ timeship, and Kalicum threatens Chloe’s life, forcing Jamais to transport them back before the start of the Universe. He then returns to the null chamber, where he uses Trix as a human anchor to keep Guy’s metabolism stable while he implants the diamonds in his body. He still believes Trix to be an old lady, however, and when he wakes her after the operation, she is able to catch him off guard and knock him unconscious.
The Timeless building transforms into the shape of a tree and begins to dematerialise, but with Chloe and Jamais’ help, the Doctor and his allies force their way inside before it vanishes completely. Erasmus’ death has destabilised the net holding Chloe and Jamais, and Jamais is thus able to extend himself to transport the Doctor’s TARDIS back with them as well. Chloe reassures her dolly that everything will be all right, and when the jealous Jamais snaps at it, the Doctor takes it from her so as not to distract the animal.
Sabbath boards the Jonah to confront Kalicum again, but the Doctor uses the transmat which Kalicum had used to transport the diamonds into the null chamber and gets there first. He sends Trix out to delay Sabbath while he tries to help Guy, and although unhappy to find herself in this situation, she manages to surprise Sabbath, stick him with one of Fitz’s abandoned tranquilliser darts and flee, pursued by the angry apes. The Doctor finds that he’s too late to reverse what Kalicum has done to Guy -- or so he thinks until he realises that Guy is still carrying the “miracle cream” which the Doctor had used to heal his burns and which Guy had subsequently used on Pete. By the time the dazed Sabbath arrives, the Doctor’s work is done, and he departs, leaving Sabbath to confront the recovering Kalicum. Kalicum refuses to explain or indeed identify himself, and he transports the dwarfstar cylinder into the void, transforms into crystal and disintegrates. Sabbath flees for the bridge, vowing to escape and find out the true nature of his “allies”.
The Timeless ship materialises in the void before the Big Bang, but the strain of taking them there is too much for Jamais, who apparently dies. His death destabilises the mesh further, enabling Anji and Fitz to free Chloe -- and Jamais then revives. Reunited with Trix, they head out into the void to free Guy from the dwarfstar cylinder, only to find that it now contains Chloe’s doll. The Doctor arrives with the recovering Guy and explains that the “miracle cream” patterns itself upon the patient’s DNA in order to replace damaged cells with healthy ones; by coating the doll with the cream, the Doctor tricked the diamonds into believing that the doll was Guy, and was able to transfer them out of his body and into the doll. He and his friends head back to the TARDIS, intending to analyse the diamonds and find out the true nature of Sabbath’s allies, but Jamais again becomes jealous of the attention being paid to the doll -- and before anyone can stop him, he seizes the doll and tosses it towards the singularity. The Doctor and his allies get back to the TARDIS just in time, but, whether by accident or design, when the Universe is born this time it’s imbued with the alien essence from the diamonds.
Jamais breathes the TARDIS back to safety, but the strain has indeed been too much, and he will never be able to travel through time again. At Chloe’s request, the Doctor sets the Timeless ship to drift through the early years of the Universe, giving Erasmus an eternal tomb. Back in the 21st century, Daniel Basalt is in a coma, and Guy’s nephew Pete has fully healed -- but is now the spitting image of Guy himself. Anji returns to her normal life at last, and throws a farewell party for her friends; even Stacy attends, for though shaken by the revelation that she owes her happiness to the death of an alternate self, she has decided not to waste the life she has. Trix, still intrigued by the opportunities time travel offers her, decides to keep travelling with the Doctor, and before leaving she gives Guy the next day’s winning lottery ticket. Guy reports Mike to the police, quits his dead-end job and prepares to experience life to the fullest instead of just coasting through it as he has in the past. The Doctor, Fitz and Trix set off to investigate the origin of Chloe’s lost locket, which she claims to have received from a Russian princess -- and Trix leaves Anji with forged adoption papers which will enable her to become Chloe’s legal guardian, as Chloe just wants somewhere to settle down. After some reluctance, Anji decides to accept the responsibility, and embarks on her new life as a mother.