On the night of 13 October 1910, Edgar Miller breaks into a house in London. He makes his way from room to room, filling a sack with valuables. When he reaches the bedroom he stares in horror. Two people are lying in the bed, dead. Their faces have horrified expressions and their eyes are bleeding. Standing over them is a humanoid figure: spindly, red eyed and with needle sharp teeth. Miller flees down the stairs and into the kitchen. Three more of the creatures are standing there. One of them tells him they are Squall and that it is time to feast. Blood bubbles from Miller's eyes.
The TARDIS is making a hectic journey, bumping and vibrating as it goes. Rory asks what is happening but the Doctor can only tell him that it is in a hurry. It lands suddenly with a bump. The Doctor flings open the doors and steps into the sunshine to find where they are.
Rory follows and sees a bright futuristic city. He recognises from some of the older buildings that it is London. The Doctor guesses that they are in the twenty-eighth century. He is still wondering why the TARDIS came in such a hurry. Amy points to the bank of the Thames below them. Some people are pulling something out of the water. The three of them walk down to see what is happening.
On the bank are a team of archaeologists. Some are ducking in and out of tents and others cluster round the thing from the river. A middle aged woman who appears to be in charge asks if she can help the newcomers. The Doctor flashes his psychic paper which apparently tells her they are inspectors from the city conservation board. The woman introduces herself as Patricia Young. She indicates the thing that has been dragged from the water and says that it is an extremely expensive artificial intelligence unit which someone has dumped in the river. The unit is humanoid but missing an arm and the lower part of a leg. The Doctor scans the unit and asks Patricia how long these units have been on sale. When she tells him that it is only two or three months he replies that this particular unit has been in the water for centuries.
The Doctor notices that there is still some residual power in the unit and uses his screwdriver to activate it. The unit turns its head towards the Doctor and says his name. It tells him that it has waited a thousand years for him, adding that the Squall are coming and that Gradius's experimental ship has torn a hole in time. It tries to say something about the hive manifesting in the path and something that the Doctor told it but its power cuts out and the unit crumples.
The Doctor says that the last of the power has gone and the unit's neural matrix will have collapsed. He guesses that this unit is the reason why the TARDIS brought them here. Amy wonders how it can think the Doctor told it anything but the Doctor thinks that this must be an event from his future. She asks who the Squall are. He says that they are a race of parasites that live outside the normal universe. They try to get into the real universe and feed on psychic energy to establish their hives.
He tells Amy and Rory that they need to find Gradius and put an end to his time experiments. While they are doing this he will take the TARDIS back to the day before the unit ended up in the river. He calculates from a sonic reading that he needs to go to 16 October 1910. He blithely assures Rory that it is a simple matter of plugging a hole in the universe, stopping a murderous horde of aliens and popping back to pick them up. He runs back to the TARDIS.
On the night of 16 October 1910, Professor Archibald Angelchrist sets out to find the creatures that are responsible for a string of murders in London. He has been retired for five years but has gained enough knowledge to conclude from newspaper reports that the murderers are alien. He has fought aliens before on a number of occasions and finds reports of bipedal demons on the streets of the city no more alarming than anything else he has faced. He has worked out that there are at least three creatures on the loose, each working within its own territory. He drives his car down to a likely place to find one.
Striding out into a cold, foggy night he makes his way to the river. Almost at once he finds the creature and waits for its attack. He beats at it with his walking stick but is alarmed when its talons grip him and he feels it probing him telepathically. He strikes it hard with his cane and seems to have regained the advantage when the Doctor arrives with his sonic screwdriver. The creature backs away and flees into the fog.
Angelchrist is initially angry at the Doctor's intervention. However, he is soon won over by the fact that the Doctor seems to know more about them than he does. When the Doctor learns that Angelchrist was hunting the creature, and has fought aliens previously in his job for the secret services, he shares some information: he tells the old man that they are the Squall, there are far more than three of them and that they are pouring in through a rent in time. The professor says that he has mapped out the area of their activity and takes the Doctor to his car, saying that he will drive him back to his house to see it.
It takes Amy and Rory a day to negotiate the city streets. On the way they pass what appears to be a zoo with glass domes, but Amy recognises it as an oxygen factory. Eventually, they enter an information booth and track down Professor Gradius. They make their way to the headquarters of Gradius Industries which seems to be a large, empty warehouse near the British Museum. In the centre of a huge hangar they see a huge space ship. As they walk round it they find a dead woman. She is wearing a white lab coat and her eyes are weeping blood.
The Doctor looks at the map in Angelchrist's study. It shows the sites of six murders. The Doctor decides that the place they want is near to the British Museum. The professor agrees to join the Doctor for one last adventure. They take the professor's car. On the way they see three of the Squall circling in the skies overhead. After half an hour of driving round the area near the museum, the Doctor parks the car. He leads the professor to an alleyway and kicks open a gate. They see, buried in the wall of a house, a silver space ship that the Doctor says is Gradius' time ship. The professor is puzzled that the wall of the house has not been damaged but the Doctor says that he is more surprised the neighbours haven't noticed. It is then that they see the eaves of all the houses are filled with the Squall. As the aliens close in the Doctor notices one of them is holding Amy's jumper. He holds the screwdriver up and it emits a high pitched squeal that drives the aliens back. The Doctor tells Angelchrist that the power will drain soon, so now is the time to run.
Back in June 2789, Rory searches the dead woman's pockets and finds an ID card showing that she is Professor Celestine Gradius. They hear a knock from a trapdoor in the floor. An AI unit pops its head out of the hole. It tells them that it is Gradius' assistant, RVN-73. Amy promptly christens it Arven. It says that it tried to help the professor fight off assailants but when it was overcome it threw itself down the hatch. The last thing it heard was the professor telling the attackers to get out of her head. Rory wonders who the attackers were. As if in answer a mass of the Squall come down the stairs. Amy suggests that they hide in the ship. Rory and Amy climb aboard while the AI holds off the Squall but Amy gets out again to rescue the unit. Rory helps her and they pull Arven through the door and slam it shut. As the Squall try to tear through the hull Amy orders Arven to fly them to 16 October 1910. He warns them that the ship has only been tested on flights of a few minutes but agrees to do what they say.
The Doctor and Angelchrist drive at speed through the foggy streets. As they drive, the Doctor tells Angelchrist that the Squall are hive creatures: basically a single organism with the individuals merely drones that feed the hive on psychic energy. The hive mind divides between the drones so that three or more together are intelligent enough to communicate. The Doctor says that the time ship is what allowed them to break through to Earth. He also says that the Squall have a psychic dampening field that renders them almost invisible until they pounce. There could be thousands of them in London and nobody would know they are there unless, like Angelchrist, they were expecting to see them. Eventually the Doctor parks the car and strides through foggy alleyways to find the TARDIS. Unfortunately, when they reach it, the Squall are swarming over the big blue box, drawn by its energy. One of the aliens sneaks up on the two men and attacks the Doctor. He drops the screwdriver but Angelchrist picks it up and uses it to drive the Squall off. The two men run.
When they get back to the professor's house they have a cup of tea and then the Doctor sets about using the professor's workbench to make something useful. By morning he has built an amplifier for the sonic screwdriver so that he can get back into the TARDIS. Before that, however, he needs to find Amy and Rory wherever they are in 1910.
Rory and Amy wake in a dark space. They ask Arven to switch on the lights but he tells them that half of the control panel is missing. Apparently they have materialised inside a wall and the control panel, along with Arven's arm, is part of the wall now. There is no way of reversing this process so Rory has to amputate the Ai's arm at the shoulder. The three of them exit the ship but Amy's red jumper snags on the buckled metal and she discards the garment when the first of the Squall arrives through a shimmering haze: the rent in time.
The three of them run up a busy street to escape. The sight of the battered Arven, his flesh in tatters, his arm missing, causes some distress to passers-by. As they pass a news vendor Amy snatches a newspaper. When they finally stop by a churchyard they find that they have arrived three days early on 13 October. To their horror, three of the Squall are still in pursuit. They run towards the church and close the doors against the aliens. While Arven holds the doors closed, Amy and Rory search for another exit. They find steps going down. While they debate whether to explore, Arven races up to them telling them that the Squall are inside.
They find themselves in a long tunnel that leads past some very old coffins and then worms its way under the ground. It eventually connects to the sewers and from there they climb a ladder that lets them out on a sunlit street.
For three days they move from place to place. They steal a coat to hide Amy's ultra-short skirt and a cap to hide Arven's ravaged face. They have to keep moving for the Squall always seem to find them. At one point they enter a deserted house only to find the corpse of a burglar in the kitchen and the Squall already waiting for them. Eventually they take refuge in a boarded up house in Whitechapel. Rory reminds Amy that it is now 17 October, the day that the one-armed AI in 2789 told the Doctor it ended up in the Thames. At least, points out Rory, they know that Arven is going to meet the Doctor later that day. As such, they make their way from the house to the river. The hope is that the Doctor will go to the river, too, for his predetermined date with Arven. As they wait, the Squall closes in on them. There seems no hope of escape.
The Doctor arrives, with Angelchrist in tow, and uses the screwdriver and amplification device to incapacitate the Squall. He switches it off, tells them to go and allows them to run away. Amy, naturally, berates the Doctor for being three days late before telling him that the Squall were in the twenty-eighth century, too. The Doctor introduces the professor to his friends and Amy introduces Arven. It dawns on Amy that she was responsible for creating the rift that allowed the Squall through. Rory thinks that this is a paradox but the Doctor tells him that time doesn't work like that. He says that there are fixed points but other than that time flexes around those points.
The group walks back to the TARDIS. The professor warns the Doctor that they are walking into a trap but the Doctor replies that if they know it is a trap then it can't be one. As the Squall close in on them the Doctor is appalled to find that the amplifier no longer works. The Doctor remembers that when Arven was pulled from the river it told him to modulate the frequency. He does so and the Squall fall back. The Doctor opens the TARDIS door and the group step inside. Angelchrist is astonished by what he sees but the Doctor is quick to get onto the console where he is disappointed to find that the rift is already too big to close by simply flying the TARDIS through it. He needs to think of a new plan.
The Squall use the TARDIS telepathic circuits to tell the Doctor that they intend to take London in a matter of hours and then use the TARDIS to dominate the universe. The Doctor decides it is time for plan B and hops the TARDIS over to the other side of London and materialises in Angelchrist's laboratory. While the professor makes tea and sandwiches for his guests, the Doctor starts to improvise a new device. All too soon, the Squall come crashing in through the window. Arven and the humans begin piling furniture against the window to keep them out. The Doctor appears, wearing a top hat. Amy tries to tell him that this is not the time for new headgear but he lifts the hat and shows a tangle of wires underneath. He tells her that this is Plan B.
He tells her that the Squall have tasted his mind. While human minds are juicy morsels, their real goal has become his big Time Lord brain. He has made the hat into a booster for his psychic signal so that all of the Squall are attracted to him. That way he can lure them back to the rift and put them back where they came from. He then intends to use the Gradius time ship to seal the rift with an implosion. As he tells them this he enters the TARDIS and manipulates some of the controls but tells them that the TARDIS has to be kept away from the Squall in case they exert an influence over it and from the rift in case the implosion pulls it through.
Arven tells them that he has learned enough from their conversations to know that their past is his future and that somehow he will make it home to his own time. He volunteers to create a distraction so that the others can get to Angelchrist's car. The Doctor makes some adjustments to Arven with the sonic screwdriver and the others say goodbye to the AI unit. He then opens the door and fights his way out through the Squall. As he hoped, the Squall follow him and the others exit the house via the cellars. As they get into the car they see Arven up the street, now reduced to little more than a metal skeleton as the Squall rip him to pieces. As the car drives away, a cloud of aliens forms in the sky above, giving chase.
The Doctor drives quickly if erratically while the other three use a variety of weapons they have brought to fight off any of the Squall that get too close. Eventually he arrives at the house where the time ship crashed. He smashes the car through a wooden gate and leaps out and into the ship. The cloud of Squall descend and fight their way into the ship. As the others watch in horror, one of the Squall emerges with the limp form of the Doctor, his clothes shredded. Angelchrist leaps top help him as there is a rending sound and the world turns white.
Amy and Rory find themselves lying in the garden of the house. There is a hole in the wall where the ship was but it, the Squall, Angelchrist and the Doctor have gone. Before they can begin to grieve, the TARDIS materialises beside them. Amy opens the doors and sees the wreckage of the time ship in the control room. Lying unconscious among the wreckage are the old professor and the Doctor. The Doctor sits bolt upright and asks if the Squall have gone, then checks the scanner to see if the rift has closed.
He tells them that he programmed the TARDIS to scoop the time ship away at the moment of the implosion. When Rory says that he thought the TARDIS had to be kept away from the implosion the Doctor replies that he knew the Squall were listening via the telepathic circuits so he told a clever lie that prevented them seeing his true plan.
The Doctor offers Angelchrist a lift home but the professor asks if he may see the universe properly from above. The Doctor agrees. Soon, Angelchrist is standing at the TARDIS door looking at the stars. Next, the Doctor takes them to the twenty-eighth century where they land by the Thames. While the professor is astonished at the London he can see, Amy and Rory are more taken by the sight of themselves and the Doctor on the embankment. The Doctor tells them that the TARDIS originally brought them to that point in response to a distress beacon he created in Arven just before the AI left to distract the Squall.
As soon as the earlier versions of themselves have dispersed, the Doctor leads Amy and Rory, followed by Angelchrist, to the remains of Arven. The Doctor pulls a metal cylinder from Arven's chest: a back-up memory. He pockets it and then says that it is time to take the professor home.
In London, 23 October 1921, Angelchrist reflects on the last ten years of work with the secret service and Scotland Yard. He thinks of the various mentions to the Doctor he has uncovered in that time in the secret files he has seen. He thinks about the various faces the Doctor seems to have worn. Just then, there is a knock on the door. He opens it to find the Doctor asking if he can have the sonic wrench he left behind. The Doctor is astonished to find that ten years have gone by. However, he presents Angelchrist with a newly repaired and pristine Arven and asks if the AI can stay with the professor because his kind won't be granted their liberty for at least two centuries. The professor is delighted to have the company.