On its way back from Endpoint, the TARDIS is shaken by a bout of severe turbulence, and the Doctor is forced to shut it down, realising that it’s tearing itself apart trying to break free from some force which is trying to make it materialise. He, Fitz and Anji emerge to find that they have landed in a war-torn wasteland, where they are captured by Defaulter soldiers who accuse them of being Plutocrats. As the soldiers march them across the battlefield, the Doctor learns that the war is being fought with weapons capable of accelerating and decelerating Time; soldiers can either age to death in seconds, or be frozen in place for eternity.

The Doctor, Fitz and Anji escape under cover of a Plutocrat bombardment, and are rescued by an officer named Lane who assumes that the Doctor is the time expert they’re expecting to arrive from Station One. The Doctor plays along, and Lane takes him and his companions to Isolation Station 40, along with a soldier named Bishop who was caught in a time storm, and whose right arm is now centuries older than the rest of his body. Upon arriving at IS-40, Bishop is placed in a DT capsule, which decelerates Time, keeping him stasis until Doctor Hammond can determine whether it’s economically viable to let him live. All decisions in the plutocratic empire are determined by economics, including the life and death of individuals. This war is being fought because the occupants of this planet defaulted on their payments -- and because both sides have access to temporal weapons, they have been stalemated for centuries.

The Doctor and his companions meet more of IS-40’s staff, including clockwatchman Shaw, who monitors Time within the base to ensure that its defenses have not been breached. The weary and alcoholic Commander Bragg then leads them to the laboratory to observe Doctor Paterson’s demonstration of his new RT capsule; using chrononium, the time-active element which is used in all temporal weapons in this war, Paterson believes that he can travel back through Time. Two volunteers, Ash and Norton, enter the capsule and are lowered into the past, but the dive goes out of control, relative Time within the capsule slows down and Ash and Norton begin to scream. The Doctor manages to halt the capsule’s descent and raise it back to the present, but when Lane dons a Time-Resistant suit and examines the two men, she finds that they are suffering from anachrophobia, the time-travel equivalent of decompression sickness. They are placed in quarantine, but Hammond holds out little hope for them; all other volunteers have exhibited the same signs of disorientation, memory loss and physical trauma, and all have been terminated as being “non-viable”.

The Doctor examines the capsule interior and finds evidence that a breach occurred, letting Time out of the capsule -- and, perhaps, letting in something else. Norton’s condition seems to be deteriorating, and he can no longer recognise himself in a photograph, but he is not just losing his memory -- Time is passing more slowly around his body. It’s as though the soldiers have been infected, or possessed, by Time itself; Norton is not just forgetting his past, his past is ceasing to exist. The Doctor refuses to let Hammond terminate his patients, and Bragg concurs... because he feels that this “infection” can be used as a weapon. Norton, meanwhile, remembers hitting his lover Georgina, losing his temper with the woman he loved. He doesn’t want to be that sort of person, and soon, he won’t be...

As night falls, Lane, Paterson and Bragg are haunted by uneasy memories of the wasted lives and the mistakes which have led them here. Fitz, concerned for the Doctor’s well-being following the removal of his second heart, goes for a walk, only to be struck down when he finds the airlock door jammed open. When he recovers the next morning and tells the Doctor, the Doctor concludes that someone wanted to leave the base and return without anybody else knowing.

The Doctor decides to investigate Ash and Norton’s experience directly, and Fitz reluctantly agrees to accompany him on another RT dive. However, as Paterson and Anji supervise the first stages of the dive, Bragg finally manages to get through the interference caused by the time storms, and learns that the real time expert never left Station One. Already drunk and blaming himself for letting the Doctor fool him, Bragg takes Shaw and Hammond to the lab and arrests Anji, refusing to let her retrieve the Doctor and Fitz -- even when relative Time within the RT capsule begins to slow down, and something outside begins hammering at the hatchway, trying to get in...

Lane enters the quarantine chamber to check on Ash and Norton, but they suddenly try to grab her and remove her TR suit. In her panic, she tears her suit on the way out of the airlock -- and then Time slips back one minute, putting her back in the quarantine bay in a torn suit. She escapes and contacts the lab in a panic, distracting Bragg just long enough for Anji to overpower him and bring back the Doctor and Fitz. However, Shaw then overpowers her in turn, and the Doctor, Fitz and Anji are all locked up. Bragg is beginning to become paranoid, and he confines Paterson to quarters, accusing him of aiding and abetting defaulter agents. He also confronts Lane, who has just discovered that Time is beginning to slow down around her body as well. When she and Bragg slip back one minute in Time and Bragg fails to notice, this confirms that Lane has become infected as well -- and that she’s passed the infection on to Bragg.

Mistletoe, a fussy man in a bowler hat who claims to be an auditor from Station One, arrives at IS-40 to determine the viability of Paterson’s experiments. After interrogating the Doctor, Fitz and Anji, Mistletoe decides to investigate the “contagion” by placing the injured Bishop in the quarantine bay. Shaw then contacts Bragg, claiming that the prisoners have escaped, and Bragg, infuriated, concludes that Paterson is responsible. In fact, Shaw released them, for reasons of his own, and when Bragg leaves to confront Paterson, Shaw leads the Doctor and his friends into the medical bay and helps them to tie up Mistletoe and Hammond. They’re too late to save Bishop, however -- and as he too is “infected”, all three patients’ faces disappear to be replaced with the faces of clocks. As the Doctor realised when something physical tried to break into the capsule, this is far more serious than a mere infection. The Doctor uses the anaesthetic gas halothene to knock out the “patients” and examine them, and finds that their bodies appear to be turning into clocks. This is clearly impossible, and the Doctor theorises that he and his friends are perceiving something from outside Time, a force which is using the infected people as hosts and which is too alien to perceive as it really is.

Bragg confronts Paterson, who, terrified, accuses Lane of releasing the prisoners -- and hates himself for it. He too then experiences a repeated minute of Time, and flees in terror when he sees Bragg’s face transform into the face of a clock. Bragg, who has always considered himself ugly, is haunted by memories of the young, handsome soldier who cruelly taunted and rejected him. Elsewhere in the base, Lane is likewise haunted by her memories of attempting suicide on the crowded cargo liner which brought her here, and of sleeping with Shaw because nobody else wanted her. Paterson once betrayed his wife Charlotte by sleeping with another woman; he didn’t really enjoy it, but gave in to a moment of weakness and lost everything he loved. He seals himself in the lab and calls the medical bay to warn them, and the Doctor and Anji suit up and pass through the quarantine bay in order to reach Paterson without encountering Bragg or Lane. They’re too late; Paterson also has the face of a clock, and he reveals that he now has the ability to go back through his own life and correct his past mistakes. The Doctor, however, realises that in doing so, Paterson is erasing his own past and thus himself, and he will soon be nothing more than an empty shell which the alien force can possess. Realising that this is true, and fearing the consuming darkness he can sense arond him, Paterson committs suicide by leaping into the RT capsule shaft.

Shaw apparently tires of waiting for the Doctor to return, and he and Fitz suit up and leave the medical bay -- but as soon as they’ve gone, Mistletoe frees himself from his bonds and uses the halothene gas to help Hammond collect a “sample” for investigation at Station One. The base is then bombarded by Defaulters, and Shaw forces Fitz into the lower levels at gunpoint, leaving the others to fend for themselves. The Doctor and Anji are trapped behind a safety bulkhead when the base’s TR shielding is breached, and are attacked by the clock-faced Bragg. The Doctor short-circuits the bulkhead controls in order to get through, and then seals it from the other side -- but Bragg rewinds Time, taking the bulkhead back to the moment in which it was open. The Doctor, however, realises that moving Time backwards requires effort, and that the clock creatures must therefore use this ability sparingly; thus, he continues to close the bulkheads behind him as he goes, delaying pursuit while he and Anji get to the control room. There, they are reunited with Mistletoe, who is also sheltering from the clock creatures. The clock creatures arrive too late; too much time has passed since the door was closed for them to rewind it that far. But now the Doctor, Anji and Mistletoe are trapped.

Fitz and Shaw sit out the bombardment in the lower levels, and then return to find out whether anyone else has survived. They are attacked by the clock-possessed Lane, and although Shaw shoots her repeatedly, Lane rewinds her own personal Time, thus surviving and leaving Shaw with no bullets. Fitz and Shaw flee to the medical bay, but find that Lane has already released the other infected patients. Fitz contacts the Doctor, who has him and Shaw come to the control room with clockwork grenades; Shaw sets one for two minutes and rolls it towards the waiting Norton, who fails to notice it until it explodes. Mortally wounded, Norton rewinds Time and flees to safety, and the Doctor, Anji and Mistletoe emerge from the control room and run around the corner before the explosion. They then retreat to the medical bay and seal themselves in, but they’re still trapped in the base with the clock creatures, who intend to possess them all.

Anji finds requisition reports about troop movements, and when she analyses them she realises that soldiers are being sent into battles they can’t win and that others are being withheld from easy victories. Mistletoe and Shaw admit that the Plutocrats are deliberately prolonging the war to stimulate their empire’s economy and get rid of the dead wood; all soldiers in this war have been drafted from those who couldn’t keep up their payments to the empire. The Doctor wonders why the Plutocrats invested in Paterson’s experiments if they don’t want the war to be won, but that’s a problem for later; right now, they must deal with the creatures in the base. Since the use of halothene proves that the clock creatures are susceptible to gas, the Doctor decides to seal the airlock and flood the base with mustard gas. In its pure form, its effects will go unnoticed for over an hour, and by the time the clock creatures realise they’ve been fatally poisoned, too much time will have passed for them to rewind it and save themselves.

The Doctor throws a ten-second grenade into the hallway, mortally wounding the clock creatures waiting outside. They rewind time and flee, and this time, instead of tossing the grenade out, the Doctor takes Anji to the airlock while Shaw and Fitz go to the chemical stores. The Doctor successfully seals the airlock, but then vanishes while Anji’s back is turned. Unable to find him, she returns to the medical bay, where she is attacked by the clock creatures. Mistletoe saves her, letting her into the quarantine chamber and then sealing the airlock behind her. As they watch Bragg trying to override the airlock controls, Mistletoe defends the plutocratic ideal to Anji, who is disgusted by the empire’s belief that money is more important than human life. However, one thing they can agree on is that the Doctor’s heart is in the right place...

Fitz and Shaw release the mustard gas and return to the upper levels, where Fitz catches a glimpse of the Doctor in the distance. Shaw retreats to safety while Fitz searches for the Doctor, but instead Fitz finds Lane dying from exposure to the mustard gas. As the Doctor had suspected, Time is a finite resource even for the clock creatures, and going backwards takes more effort. Lane thus cannot reverse what has been done to her, and she and her fellow clock creatures all, eventually, die. Fitz finds the Doctor lying outside the laboratory with his gas mask off, and gets him back to the medical bay, where the others determine that the Doctor has not been infected by the clock creatures. The Doctor awakens, weakened by his exposure to the mustard gas and with no memory of the past hour -- but he’s still alert enough to realise that a DT stasis capsule is missing, and Mistletoe suddenly remembers that Hammond took Bishop to Station One so the “infection” could be analysed. Station One has a population of 50 to 60 thousand, and the clocks have already shown how easily they can escape from quarantine...

The survivors from IS-40 set off in pursuit, but Hammond has a six-hour head start and there are Defaulter patrols in the area. The Doctor takes the wheel, but Fitz notes that he hasn’t fully recovered from his exposure to the mustard gas, and the Doctor is forced to admit that he’s been feeling chest pains recently; perhaps his sole remaining heart is straining to do the work of two. After several hours’ drive, the Doctor catches up with Hammond’s van, which was ambushed by Defaulters; Bishop’s DT capsule was breached in the attack, and the entire area has entered a DT state. The Doctor and Anji don TR suits and search for Bishop, and find him and the attacking Defaulters frozen in Time -- but the badly injured Hammond is still capable of speaking to them, as he’s really a TR-shielded robot. Hammond is unaware of this, as he’s been programmed not to perceive the truth about himself; he knows that he’s badly injured, but he doesn’t realise that the TR shielding around his battery has been punctured, freezing its short circuit in Time.

Shaw restrains Fitz and Mistletoe in the van and confronts the Doctor outside; following the Plutocratic ideal to its logical conclusion, he is working for the Defaulters, since they’re paying him more. He infiltrated IS-40 in order to steal Paterson’s research, and released the Doctor, Fitz and Anji because he assumed they too were Defaulter agents. He knocked out Fitz earlier, to prevent him from discovering that Shaw had left the base to arrange a bombardment, under cover of which he intended to escape with one of the “infected” soldiers. He still hopes to sell this “infection” for profit as a weapon, and only ever helped keep Fitz alive so he’d have someone else who could be infected if it became necessary. He now intends to shoot the Doctor and Anji and collect Bishop, but a temporal bombardment accelerates time within the DT zone, and one of the Defaulter soldiers revives and shoots both Shaw and Bishop. Hammond’s battery short-circuits, and he explodes, killing the Defaulter. However, Bishop then rewinds Time, kills the Defaulter first, and flees before Hammond’s battery explodes. The Doctor and Anji are forced to flee as well, when Bishop’s face turns into the face of a clock...

A van of Plutocratic soldiers arrives and “rescues” Bishop before the Doctor can intervene. He and Anji return to their own van, free Fitz and Mistletoe, and set off in pursuit. They’re only ten minutes behind the other van -- but their van’s shielding has been breached, and they pass through a DT zone without realising it. By the time they reach Station One, after several more hours of driving, months have passed since Bishop’s arrival and the entire population of Station One has been transformed into clock creatures. The Doctor, Fitz, Anji and Mistletoe are nevertheless allowed to visit to the central audit bureau, as the clock creatures are in no hurry to transform them; there’s nowhere they can run.

At the central audit bureau, they meet the actuaries, automated adding machines who run the war for both sides with emotionless efficiency. The actuaries are dying, as they lost contact with the Plutocratic empire some years ago and have not received any reinforcements since then. In the centuries since the war began, they’ve forgotten the point of it, and they thus funded Paterson’s time-travel experiments in order to go back in Time and find out who they’re working for and what happened to them. Since the experiments have failed, they’ve conceded the war, and have summoned a Defaulter representative to Station One; but when he arrives, he will be infected and will carry the clock-creatures to the rest of the planet. Before the Doctor can work out how to stop the invasion, Bishop arrives -- and passes the “infection” on to him...

As the Doctor had suspected, the “infection” is a possession; one of the clock-creatures is trying to turn him into its host. He now has the ability to travel through his own past, and is tempted to change the events which led him here. He could save the thousands of people who lived in Station One by killing Bishop in the quarantine lab, or by refusing to bring back Ash and Norton from their dive. He could stop himself from giving an apple core to Silver, or travelling to the world of the poodles -- or he could stop Sabbath from removing his second heart. The temptation is almost irresistible, but the Doctor knows he can’t give in -- and when he relives a moment in the base with the possessed Paterson, he realises that Paterson is describing creatures who exist partly outside Time. The RT capsule tore a breach in the fabric of Time, letting them in, and they require the fissure in order to exist in this reality. By loading the RT capsule with chrononium, launching it into Time and detonating it, the Doctor can accelerate Time within the Vortex and seal the fissure, destroying the clock-creatures -- but IS-40 is over two days’ drive away, and the Doctor will never make it back in time...

The Doctor thus takes a terrible gamble, and returns to the moment in which he and Anji sealed the base’s airlock. When Anji turns her back, the Doctor hides, giving her the impression that he’s vanished. He then makes his way to the lab, evading Fitz on the way, and once there, he loads up the RT capsule with chrononium and rigs up clockwork timers to the capsule and to the controls in the lab. He then removes his own gas mask and deliberately exposes himself to the mustard gas; the shock serves to mask his subsequent memory loss, which was in fact caused by his future self’s interference in his past. History thus unfolds exactly as it did, unchanged, up to the present moment, at which point the timers drop the RT capsule into the shaft and detonate it, sealing the breach. The clock-creatures, cut off from their lifeline, are all killed, including the one trying to possess the Doctor.