A high-speed train travelling from Lancaster to Kingís Cross unexpectedly collides head-on with another train that wasnít there a moment before. Elsewhere in the country, Sir Alistair Gordon Lethbridge-Stewart is alone at home while his wife Doris visits her ailing sister. The press has stopped hounding him, apparently having decided that the press conference with the Silurians was some kind of hoax -- or so Sir Alistair thinks until he turns on the TV to see that theyíre now occupied with the devastating train crash outside Oxford. As he watches the news report, however, something odd happens -- and Sir Alistair discovers that heís somehow lost half an hour. Meanwhile, Chaudhry and Hoffman show up at the scene of the crash to find Francis Currie reporting for the BBC. Chaudhry refuses to make a statement until her teamís investigation is complete, but though she claims that UNIT was simply called in because it was the closest military operation to the scene, Currie isnít convinced.
Elsewhere, one Professor Meade and his assistant, Bernard Kelly, have hit a dead end in their attempts to reverse-engineer alien technology and develop a method of transmitting matter through space -- and although Meade refuses to admit it aloud, he privately fears that their experiments may somehow be responsible for the train crash. Theyíve been working from blueprints stolen from UNIT, but Earth-made materials simply canít handle the demands of the experiment; however, Kelly now informs Meade that their superiors have acquired the actual spaceship, and although the bulk of the ship is to be studied elsewhere by other scientists, they will first be allowed to remove the equipment they require. Meade knows better than to ask how his superiors got their hands on the ship, and once itís delivered, he and Kelly take what they need and leave the rest where it is. But their tampering has disturbed something, and after they leave the room, some sort of gas begins to hiss out of the ship...
Chaudhry and Hoffman examine the bodies found in the wreckage, and find that every wristwatch on the southbound train stopped just after 11:30 -- which is odd, since the crash occurred just before 11:00. Also, according to the rail company, the automatic signals and passenger ID scans indicate that one of the trains must have travelled over 40 miles in under two minutes. Back at UNIT HQ, Chaudhry receives upsetting orders from the government: UNIT is to leave Brimmicombe-Woodís kidnapping to the police and military intelligence, and concentrate its efforts on investigating the train crash. Frustrated, Chaudhry sets off for the morgue with Hoffman to investigate reports that the undertakers have found something odd about the bodies.
Kelly and Meade manage to install the alien component in their own equipment, and prepare to conduct another trial run. If successful, they will have developed a way to transport food and medicine anywhere in the world instantaneously... but Kelly more cynically points out that the device could also be used to transport troops and weapons. Meade dismisses Kellyís ethical concerns and concentrates on the experiment -- and this time, he and Kelly succeed in transporting a lead block from one test cubicle to another. There is a momentary power surge, but it isnít nearly as strong as the last time, and Meade rushes off to report his experimentís success. Kelly doesnít bother to point out that everything that happens in this laboratory is probably being monitored anyway. Elsewhere, Sir Alistair experiences another strange time-jump, and calls up UNIT, certain that this is not just his imagination. He is unable to contact either Brimmicombe-Wood or Chaudhry, however, and logs onto his home computer to find out for himself whatís going on at UNIT.
Something causes cashpoints throughout the city to start dispensing free money, and riots break out as the public try to take advantage of the bug. Chaudhry and Hoffman encounter one such mob on their way to the morgue, and see the rioters swarming a policeman when he tries to stop them from looting an ATM. Just as it seems Chaudhry will be forced to start firing warning shots, somebody else does so, driving off the mob. This is Colonel Robert Dalton of the regular army, who reveals that heís been trying to locate Chaudhry; heís been pulled out of Syria on short notice to act as UNITís temporary CO in the absence of Brimmicombe-Wood. Chaudhry arranges for the injured policeman to be sent to hospital, and she, Dalton and Hoffman continue on to the morgue.
Chaudhry tells Dalton about the anomaly with the watches, but he scoffs when she suggests that one of the trains may have travelled through Time. He doesnít know much about UNIT, and is wary of the organisation, knowing only that it seems to consider itself above the law; however, heís clearly not prepared to accept the answers Chaudhry has for him. In the morgue, they find that the bodies of the crash victims have physically merged with the debris from the trains; in one case, clothing from a suitcase is inside a manís body, mixed up with his internal organs. Dalton orders Chaudhry to send the bodies for analysis, but while he speaks with the undertakers, Chaudhry orders Hoffman to pull Daltonís file once they get back to UNIT HQ. Chaudhry and Hoffman have an easy working relationship -- but neither is sure whether they can trust their new CO.
As Kelly and Meade celebrate their success, an alarm sounds on their equipment, and they discover that the energy residue from the experiment is building once again. Any attempt to regulate the energy flow could damage their equipment, and Kelly thus suggests that they let the flare-up run its course; people will die in any case, and this way theyíll die for a purpose, as Kelly and Meade will be able to observe the energy wave and get the data they need to control it in future. Meade reluctantly allows Kelly to talk him into letting this happen, feeds his incomplete equation into the computer and sets the sensors in the lab to monitor the progress of the energy build-up. Elsewhere, Sir Alistair prepares to spend the night parked in his car; heís unsure what heís waiting for, but is convinced that his experiences will be repeated.
Back at UNIT HQ, Chaudhry and Hoffman read Daltonís service record and discover that he once served with Andrea Winnington. Suspicious, Chaudhry pops in to see Dalton before setting off for the night; thereís little more she can do here until sheís heard back from the labs analysing the bodies. Dalton is surprised that UNIT has no facilities to conduct such analysis in-house, but Chaudhry explains that their budget has been slashed by governments that didnít approve of their international nature. She notes that Dalton still doesnít consider himself a part of UNIT, but when she asks him about Andrea Winnington, he seems to have no problem with confirming that they served together some time ago -- and claims that he found her rather intense. Chaudhry leaves for the night, still unsure whether Dalton can be trusted.
The next morning, Meade is woken by a strident alarm from the laboratory; the power is building more quickly than he or Kelly had expected. The extra data allows him to complete his equations, however, and he and Kelly finally realise that by manipulating the dimensions of space, theyíve inadvertently been affecting the dimensions of Time as well. Kelly, furious with himself, lashes out at Meade for failing to spot this, and Meade finally realises that Kelly is far more than just his laboratory assistant. He tries to use his equation to power down the equipment, but Kelly stops him from doing so, revealing that he has orders to destroy the lab and leave no evidence of his experiences. Despite Meadeís protests, Kelly forces him out of the lab and lets the energy flare-up run its course. Some distance away, the crew of a jet plane beginning its final approach to Heathrow find that they are suddenly no longer at 35,000 feet...
Chaudhry returns to UNIT to find that Dalton has worked through the night and fallen asleep at his desk. The military police have asked to speak with the men who were on escort duty with Brimmicombe-Wood, and Dalton has to brief them on what they can and canít say -- but to Chaudhryís despair, Dalton had assigned a low priority to the case and doesnít know what they were escorting or why itís so secret. However, they soon have bigger things to worry about. The jet plane has crashed into Windsor Castle, killing two members of the royal family -- and many other incidents occur simultaneously across the country, including an explosion in a retirement home. With no explanation for these disasters, the media begins to speculate, and Francis Currie is among those wondering whether Britain is under attack by terrorists.
Sir Alistair experiences another time surge, and plots his own experiences onto a map of the recent incidents. When he compares his findings to recent satellite photographs of the country, he finds radiation spikes that coincide with the train and plane crashes -- as well as with the glitch in the cashpoint system, which may have been caused by an EMP. He e-mails his findings to Chaudhry, who takes them to Dalton but does not tell him where she received the information. Hoffman determines that the spikes originated from an industrial complex owned by an obvious dummy corporation named British Amalgamated, and the UNIT troops set off to investigate. Halfway there, however, they pick up an urgent distress call from Basildon naval base; the reactor aboard the research sub HMS Perthshire has been breached and is going critical. They canít take the risk that itís a false alarm sent to divert them from their investigation, and Dalton thus splits his forces, taking half the troops to Basildon with him and sending the rest with Chaudhry and Hoffman to the industrial complex.
Meade and Kelly return to their lab to find the equipment falling apart, as if itís aged centuries within seconds; the only hardware that survived undamaged is the component from the alien ship. However, too much of the equipment remains intact, and Kelly realises that heíll have to find some other way of destroying it. He now reveals to Meade that he spent ten years working on this project for ICIS only to hit a dead end, which is why Meade was called in -- and now that heís finished his work, Kelly no longer has to pander to his ego. The UNIT troops then arrive at the base, and Kelly tells Meade to wait in front of the hidden escape tunnel while Kelly makes sure that the doors are secure. As the sound of gunfire gets closer and Kelly fails to return, however, Meade realises that there is no hidden escape tunnel and that heís been left behind as a scapegoat.
Chaudhry and Hoffman inadvertently trigger motion sensors as they approach the complex, and find themselves under fire as soon as they arrive. Hoffman organises a counter-attack, and his troops manage to blow a hole in the side of the building. The defending troops retreat so as not to be captured, and the UNIT troops enter to find Meade waiting in the laboratory. Realising that heís been abandoned -- and that the remote control that Kelly claimed would open the escape tunnel must be something else entirely -- Meade gives Chaudhry some of the equipment that Kelly was forced to leave behind so she can use it in her investigation. However, he refuses to leave with them, claiming that heís been responsible for too much death and doesnít want to spend the rest of his life in jail. He presses the button on his remote control, and Chaudhry and Hoffman have no choice but to retreat. Moments later, the laboratory explodes, taking with it Meade and all evidence of his experiments. In the meantime, Kelly has taken advantage of the delay to escape with the data from Meadeís experiments.
Dalton and his troops arrive at Basildon to find that the Perthshireís reactor is going to explode within hours, rendering much of England uninhabitable for centuries. Dalton thus orders Lieutenant Dodds to get the refit crew back on board and take the sub out to sea; at maximum speed, theyíll be able to reach an offshore continental shelf before the reactor goes critical. As they near their destination, Dodds shows Dalton how to work the torpedoes and then orders the others to evacuate. However, someone must remain behind to scuttle the sub, and when Dalton refuses to order anyone else to die in his place, Dodds sends the rest of the crew to safety and stays behind to help Dalton. Meanwhile, Chaudhry and Hoffman learn what Dalton has done and fly out to the area in a helicopter to monitor the subís progress. The sonar becomes clouded when the sub fires its torpedoes at the seabed, raising a cloud of dust; however, Hoffman sees enough to know that the sub went over the shelf just before the torpedo strike caused the edge to crumble and collapse. The ensuing landslide buries the sub under millions of tons of rock, and the radiation is contained when the reactor explodes. Moments later, something surfaces from the cloud of dust; the Perthshire was a research sub, and Dalton and Dodds managed to get to the bathyscaphe and escape.
This marks the end of the bizarre incidents plaguing the country, but as no explanation is offered, most of Britain remains under the impression that they have been attacked by terrorists. Dalton is peeved to find that the media, including Currie, are all but blaming UNIT for their failure to explain what happened, when it was they who saved the country. Chaudhry notes that Dalton is beginning to count himself as one of the team, and he admits that heís found out what happened to Winnington and now understands why Chaudhry didnít trust him at first. He reveals that he never really liked Winnington himself, which may be why he was assigned to UNIT. Now that the troops have seen that Dalton is willing to sacrifice himself to get the job done, even though he has a family, theyíll be more willing to trust him, and Chaudhry thus gives him some old classified files that she claims will give him the answers heís looking for. To his astonishment, Dalton finds out exactly what happened during the London Underground incident and Project Inferno, and sees that the unbelievable reports have been signed by top-ranking military officers and Prime Ministers. Dalton begins to realise heís in over his head...