On an oilrig off the coast of Scotland, a strange, high pitched beeping sound echoes through the structure, and it begins to break apart, collapsing into the North Sea.
The Fourth Doctor, Harry and Sarah hitch a ride with a passing motorist to the town where the Brigadier and UNIT have set themselves up in an inn. The Brigadier is talking to Huckle, an official of Hibernian Oil, who owned the rig. Huckle complains that three such rigs have been destroyed in the last month, two of them belonging to Hibernian. The Brigadier assures Huckle that UNIT is also concerned, especially about the loss of life.
The Doctor, Harry and Sarah arrive at the Inn. It turns out that their ride is the Duke of Forgill, a local landowner. The Duke warns Huckle that if his men are caught trespassing on his land, they will be shot. He also wants to know what UNIT are doing here, but the Brigadier says that it is a sensitive matter. Though not pleased, the Duke leaves.
On the shoreline, a survivor of the destroyed rig washes up, just barely alive. The Brigadier brings the Doctor, Harry and Sarah to Hibernian Oil, where Huckle briefs them on the injuries of the rigs' crew. Harry decides to examine the injuries at the Sickbay, while Sarah goes to talk to some of the locals. Huckle cannot understand it: the rigs were designed to be unsinkable, and the seas were calm and empty prior to the incidents. The Doctor darkly notes that the sea is never empty.
Back at the Inn, Sarah talks to Angus, the landlord. Sarah admires a stuffed stag's head above the fireplace, a gift from the Duke just this past week. Angus observes that the Duke has not been himself since the oil companies came. His servants have left to work for them, leaving Forgill Castle cold and empty. All this while, something alien watches her and Angus on a monitor screen. Angus tells Sarah about Tulloch Moor and how people have disappeared over the centuries when the mist came down. Sarah is sceptical, however — evil spirits do not destroy oilrigs.
The rig survivor, Munro, is spotted by the Duke's man, the Caber, as Munro staggers from the surf. Harry is driving by and sees Munro too, and goes to him as Munro collapses. Before Munro can tell Harry about what smashed the rig, the Caber fires a rifle, killing Munro and creasing Harry's forehead with a second shot. Harry falls, unconscious. Back at the Inn, the Doctor is working on a radio probe to check for localised jamming when a call comes in informing them about Harry.
Alien hands manipulate strange, organic controls. A high pitched beeping summons a creature from the depths that heads towards the Ben Nevis rig. The rig's communications with Huckle are suddenly jammed by the beeping.
The Doctor and Sarah visit Harry, who is sedated and being looked after by Sister Lamont, the nurse. The Brigadier arrives, telling him of the Ben Nevis rig's destruction. Sarah stays with Harry while the Doctor goes with the Brigadier. Outside, the Doctor spots a piece of wreckage from the earlier rig with some odd holes in it. The Doctor asks Sergeant Benton for some plaster of Paris, and makes a mould of the holes, revealing that something with very large teeth had bitten into the rig. The aliens, watching, decide that the Doctor knows too much and must be destroyed.
Harry awakens. Sarah goes to inform the Doctor, while Sister Lamont tells Harry that he will be very well looked after. A high-pitched beeping echoes through the room, and Harry looks up in fear. As Sarah calls the Doctor, a suction-tipped hand clamps down on her shoulder. She turns and is grabbed by a large, orange biped: a Zygon.
The Doctor hears Sarah's cries over the telephone and rushes over to the Sickbay. When they get there, Sister Lamont tells them that she found Sarah gone and Harry's bed empty. The Doctor snoops around further, and finds Sarah hiding in a decompression chamber. As Sarah starts telling the Doctor about what happened, a Zygon locks them in and starts to remove the air from the chamber. The Doctor hypnotises Sarah into not needing to breathe, then places himself in a similar trance.
Harry is brought to the Zygon ship deep underwater, where he meets their warlord, Broton. Harry is told that centuries ago, their spaceship was damaged and they landed on Earth. They were waiting for rescue when they heard that their world had been destroyed in a stellar explosion. Now, they intend to claim Earth for their own, using the sea monster under their command, an armoured cyborg of great power. Broton explains that the Zygons depend on the lactic fluid of the Skarasen, and Harry realises that if the monster is destroyed, the Zygons will die. Broton declares that no human weapon can affect the Skarasen.
The Brigadier is briefing one of his officers at the Inn when gas floods the room, knocking them all out. Meanwhile, Benton has found the Doctor and Sarah. He manages to open the pressure door, and with air restored, the Doctor exhales and awakens, carefully reviving Sarah. He tells Benton that the trance was a trick he picked up from a Tibetan monk.
Benton, Sarah and the Doctor discover that the entire village has been drugged by some kind of nerve gas, but they soon revive. The Doctor deduces that this was done so that something could get around unseen. The Zygons watch Huckle give the Doctor a device he found in the wreckage: the signal device that summons the Skarasen. Broton says it must be recovered. Harry is taken to another room in the ship, where he sees other humans hooked up to booths, providing the Zygons with "body prints" that they use to assume human form.
The Doctor hypothesises that the signal device sends out a kind of primeval mating call, attracting the beast to whatever it is attached to. The savaged body of a UNIT soldier is found on the Moor and the Doctor and the Brigadier go to see it, leaving Sarah behind in case Harry turns up. He does, but it is his Zygon duplicate. He takes the signal device, saying that the Doctor asked him to collect it. Sarah notices his curious behaviour and questions him, but he pushes her aside and runs away. Sarah and some soldiers pursue him.
Sarah discovers "Harry" hiding in an upper level of a barn, and he attacks her with a pitchfork. She steps aside at the last moment and he falls, injuring himself fatally and turning back into a Zygon. The signal broken, Broton realises his man is dead, and remotely disintegrates the corpse. Harry, however, is freed from his body print booth.
Sarah wonders how the aliens knew that they had the signal device. The Brigadier orders the Inn to be searched for bugs. Seeing this, Broton in turn orders that the Skarasen be unleashed, even if it means revealing their presence on this planet. The signal device begins to beep. The Doctor grabs the device to lure the creature away while the Brigadier tries to get a fix on the activating signal.
The Skarasen catches up to the Doctor on the Moor, and he finds that he cannot get rid of the semi-organic signal device, which has fastened itself to his palm. The Brigadier manages to trace the incoming signal to Loch Ness. As the Doctor stumbles, Broton orders the Skarasen to destroy him.
Harry rushes into the Zygon control room and randomly hits the controls, causing the device to fall off the Doctor's palm and allowing him to roll out of the Skarasen's way. Since the device is dead, Broton assumes that the Doctor is, too and recalls the Skarasen. The Doctor retrieves the device and makes his way back across the Moor as the Skarasen glides away. In the ship, Harry is dragged away by the other Zygons.
The Doctor is met halfway by the Brigadier and Sarah, who tell him that the signal came from Loch Ness. The Doctor decides to go visit Forgill Castle, which is right next to the loch. They get a frosty reception from the Duke, who does not believe them when they tell him about the monster, aliens and their intention to drop depth charges in Loch Ness.
At the Inn, Angus discovers the Zygon surveillance link in the stuffed deer head that was the Duke's gift. As he tries to pry it loose, Sister Lamont enters the Inn. Before his eyes, the sister turns into a Zygon and kills him, removing the link after. Angus's dying cries are heard by Benton and some UNIT soldiers, who discover the body and go off in pursuit of the killer. The UNIT troops sweep through the nearby forest, and fire on the Zygon.
The Brigadier is informed that a Zygon is being cornered. He and the Doctor leave Sarah behind at the Castle to research into the monster. In the woods, the wounded Zygon disguises itself once more as Sister Lamont, and fools a UNIT soldier long enough to knock him out and steal his jeep. At the Inn, the Doctor notices the missing eye in the deer head, and realises that the Duke might be a Zygon facsimile.
At the Castle, as Sarah examines the upper bookshelves, she triggers a hidden switch and a section of the bookcases slides open, revealing a hidden passage. She takes a torchlight and goes in, following a long dark tunnel that leads to the Zygon ship. The "Duke" (in reality Broton) discovers the open bookcase. He and the "Caber" take the wounded "Sister Lamont" down into the ship; the crew must be alerted and the intruder found and destroyed.
Exploring, Sarah finds the cell where Harry is being kept. She frees him and they sneak back to the Castle, just in time to meet the Brigadier and the Doctor. Sarah tells the Brigadier about the Zygon ship. The Doctor enters the tunnel, but does not get far a scream is heard. The Zygons emerge in their true forms, Broton telling the humans that they are leaving, with the Doctor as their prisoner. He warns them that the oilrigs were only a test; the "big event" is yet to come. Broton then retreats, sealing the entrance to the tunnel.
The Brigadier orders the loch to be depth charged, to try and bring the Zygon ship to the surface. The Zygon ship does rise, but keeps on rising into the sky, flying away.
Broton orders a jamming signal to be transmitted to block the humans' radar tracking systems. The Brigadier prepares to move his troops out, but Sarah and Harry suggest they search Forgill Castle before they leave to see if they can find a clue to the Zygons' plans. There, Sarah finds some papers that indicate the Duke is the President of the Scottish Energy Commission, but Harry dismisses the information as useless. They return with the Brigadier to London.
The Zygon ship lands in a disused quarry, with UNIT unable to track it as radar stations are knocked out all over the country. However, there are reports of a large underwater object heading South at high speed. Broton enters the Doctor's cell and, taking the Duke's form again, tells him that Phase I of the conquest of Earth is complete. A great Zygon refugee ship is on its way, but will take some centuries to arrive. In the meantime, Earth's environment must be restructured, using human labour and Zygon technology to turn it into a new homeworld.
Left alone, the Doctor rigs some of the organic technology in his cell, electrocuting himself but sending a transmission to aid UNIT in tracking the ship to the quarry. By the time Broton and his men manage to open the Doctor's cell door, the Doctor is apparently dead. However, when Broton leaves, the Doctor comes to. He makes his way to the body print chamber and frees the real Duke, Sister Lamont and the Caber.
Broton leaves the ship to plant a signal device on his intended target, which the Skarasen will then destroy, proving the power the Zygons hold. When Phase II is complete, he will broadcast his demands to the world. Inside the ship, the Doctor uses his sonic screwdriver to set off the fire sensor, triggering an alarm. When the Zygons go to investigate, the Doctor ushers the humans out of the ship, jamming the hatches on the way out and activating the ship's self-destruct.
The Brigadier has arrived, and the escapees reach UNIT's position, the Doctor shouting for everyone to get down just before the Zygon ship explodes. However, Broton is still out there and has control of the Skarasen. The target is in London, and has to be close to the River Thames. The Brigadier says that Prime Minister will be attending a conference at Stanbridge House, near the river. The Duke adds that it is the 1st International Energy Conference, with delegates from all over the world in attendance. As the Duke is the President of the Scottish Energy Commission, Broton will have a pass into the meeting. They leave for London.
The "Duke" places the signal device in the basement of Stanbridge House, while the Skarasen has been sighted mere minutes away. The Doctor finds Broton, back in his true form, who swears he will make sure the Doctor is dead this time and attacks him. Sarah calls for the Brigadier, who arrives to shoot Broton dead. The Doctor finds the signal device in his pocket, and feeds it to the Skarasen as it rises out of the Thames. After it consumes the device, the beast sinks back into the river and heads back to Loch Ness, the only home it has ever known.
Returning to Scotland, the Brigadier tells the Duke that the incident will be kept quiet, even the appearance of a fifty-foot monster in the Thames. The Doctor leads them into the woods where the TARDIS is, and offers all of them a lift, but the Brigadier and Harry decline. Sarah agrees on the condition they do go straight back to London. The Doctor promises, and the TARDIS takes off. The Duke tells the Brigadier that, as a Scotsman, he should have got a refund for Sarah and the Doctor's return train tickets.