Broton the Zygon warlord intends to use the Skarasen to attack London.
Broton orders a jamming signal transmitted to block the humans’ radar systems. The Brigadier prepares to move his troops out, but Sarah and Harry suggest they search Forgill Castle before they leave for clues to the Zygons’ plans. 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. UNIT cannot track it. 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 with 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 help UNIT track the ship to the quarry. By the time Broton and his men 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 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 and activating the ship’s self-destruct.
The Brigadier has arrived and the escapees reach UNIT’s position. The Doctor shouts for everyone to get down just before the Zygon ship explodes. However, Broton is still free and has control of the Skarasen. The target is in London and must be close to the River Thames. The Brigadier says the Prime Minister will be at a conference at Stanbridge House, near the river. The Duke adds it is the first International Energy Conference, with delegates from all over the world. 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. 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 to the TARDIS and offers all of them a lift. The Brigadier and Harry decline. Sarah agrees on the condition they 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 gotten a refund for Sarah and the Doctor’s return train tickets.