The Doctor rushes over to the hospital and the Brigadier orders reinforcements. The Doctor and Benton talk to Sister Lamont, who reveals he's gone but a window is open. The Doctor sends Benton to find some men to search Tulloch Moor while Lamont shows the Doctor the phone where Sarah Jane made the call. Poking around, the Doctor finds a decompression chamber and they split up to search the place. But the Doctor sneaks back to search the decompression chamber and finds Sarah Jane inside. She describes the creature she saw but they turn to see it sealing them in. The alien bumps the air out of the chamber then leaves.
In the alien control chamber, two of the aliens bring Harry in to meet their leader, Broton, Warlord of the Zygons. Broton reveals they will crush the Earth and shows Harry their intended weapon – a huge underwater creature. It becomes clear they're in a spaceship in the sea, and Broton reveals that the creature is a Skarasen which they bred and then cybernetically enhanced, and it provides a lactic fluid they need to survive.
The Doctor puts Sarah Jane into a hypnotic trance and then enters one himself. The Brigadier is receiving a report when gas fills the village, knocking him and the UNIT soldiers out.
Benton returns to the hospital and finds the decompression chamber. He pumps air back into the chamber and gets the door open. The Doctor wakes up first and then carefully brings Sarah Jane out of her trance.
Huckle arrives in the village and finds everyone unconscious. Outside a UNIT soldier is making his way through the mists when he sees the Skarasen. The Doctor and his people arrive and the Doctor concludes that someone wanted to pass the village without being noticed.
On the Zygon ship, one of Broton's underlings announces that the Doctor is still alive. He looks on through the monitoring device as Huckle reveals they found some kind of bio-organic device amidst the wreckage. The Doctor recognizes it as a signal device and Broton orders Harry be taken for a "body print." Harry is taken into a chamber where other humans, including the Duke and Sister Lamont, are strapped into machines. The Zygons reveal the humans aren't dead but rather maintained so the Zygons can become their duplicates.
The Doctor figure that the signal device emits a mating call and Huckle mentions he heard an animal outside. The Brigadier wakes up and refuses to believe he was unconscious.
Benton has found the UNIT soldier out on the moor, savagely torn to pieces. The Doctor and the Brigadier go to investigate while Sarah Jane types up her story. An odd-acting Harry arrives and immediately takes the signal device. When Sarah Jane realizes something is up, he shoves her aside and runs off through the village. Sarah Jane goes after him and rounds up some UNIT soldiers to help. Harry runs into a barn and Sarah Jane and the others split up. She follows him inside up into the loft where he grabs a pitchfork and comes at her. She manages to duck aside and Harry falls over the edge and plummets to his death. But as Sarah Jane looks on, "Harry" reverts to a Zygon, and the Zygons on the ship realize their comrade is dead. They order a self-destruct system of sorts which destroys the building.
The Doctor continues to work on the signal device and Sarah Jane wonders how the Zygons knew they had it. The Doctor has the Brigadier search the place and Broton responds by activating the signal device to send the Skarasen after them. The Doctor resolves to take the device and draw it off while the Brigadier homes in on the signal.
The Doctor drives off across Tulloch Moor then leaves on foot when then land rover gives out. Hearing the Skarasen's roar, the Doctor takes off on foot. The creature relentlessly closes in on him and the Doctor gives it up and tries to throw away the signal device. However, it's attached itself to his hand and he has no choice but to keep running.
The Brigadier and his men determine that the signal is coming from…Loch Ness. The Doctor finally collapses and Broton orders the Skarasen to finish its mission and kill the Doctor.