The episode is a continuation of Professor Travers' Tibetan expedition, in which Travers donates a Yeti (actually a robot for the Great Intelligence) to a museum. Now Professor Travers has discovered how to activate a control sphere (which controls the Yeti), and now it is missing. Travers tries and fails to get Silverstein, the museum's curator, to give up the Yeti exhibit, and is taken home by his daughter Anne. As Silverstein is closing up, however, the control sphere crashes through a window and activates the Yeti, which attacks Silverstein.
The episode begins with Salamander, an evil dictator (from the previous serial, The Enemy of the World) who looks exactly like the Doctor, hurtling out of the TARDIS while the doors were still open. The time travellers are left clinging onto the central console, and Jamie manages to move himself to a position where he can reach and operate the door controls with success.
The trio, Jamie, the Doctor, and Victoria, land after some trouble in the Covent Garden station in the London Underground. Although the station is abandoned, there is broad daylight outside. Jamie spots a newsvendor outside the gate, but when he taps him on the shoulder the old man topples dead to the ground, revealing him to be covered in cobwebs. Behind him is the headline - LONDONERS FLEE! MENACE SPREADS.
Layers of dust in the train station indicate that no trains have run down the line for some time. While searching, the tunnel is suddenly illuminated. The travellers duck into a nearby alcove. A trio of soldiers march past with an unwinding drum of cable wires. Emerging from their alcove, the Doctor tells Jamie and Victoria to follow the soldiers surreptitiously while he tracks the cable's source. They agree to meet in a few minutes.
Victoria walks into a hanging cobweb and her exclamation alerts the soldiers, who capture Jamie and Victoria.
The Doctor follows the cable as far as Charing Cross underground station. However, he is forced to hide when he hears a Yeti coming. Hiding under the platform, the Doctor is not spotted by the lumbering creature as it moves onto the station platform, holding a mysterious weapon of some kind.
Still hiding, the Doctor notes that a second Yeti has joined the first. Using their mysterious weaponry, the pair of robots cover some crates with a thick cobweb substance.
Arnold arrives with his men and their captives, Jamie and Victoria at the army's headquarters underneath Goodge Street Station. The soldiers there are concentrating on blowing up the tunnel, and Arnold, one of the soldiers that captured Jamie and Victoria, is assigned to question the pair. Anne, the Professor's daughter, worriedly tells Arnold to ask them if there was anyone with them - the last thing they want is to explode the tunnel and kill an innocent person in the process. Herding Jamie and Victoria into the common room, Arnold is reluctant to answer any questions about the situation in London. Jamie tells Arnold that he and Victoria were alone because he thinks this will result in the Doctor's capture, unaware of the real intention behind the question. However, when the two realize the military's intent, they reveal, too late, that the Doctor is still in the tunnel.
Back in the tunnel, the Yeti have finished their task and leave the platform. Stepping out from the shadows the Doctor goes to the crates to examine their handiwork. The Doctor is caught by a contained blast as the crates explode, but as the sound of the explosion subsides, the crates are still there, and glow with an eerie light.
The soldiers soon work out that the blast in the tunnel did not register in the normal way. Jamie and Victoria find out about the Yeti and contact Anne Travers, who tells her father about them. He is overjoyed to be reunited with his old friends from Tibet, but puzzled as to why they have not aged like him. Travers insists the Doctor must be found, and Jamie heads off with Arnold to see if they can find him. They soon meet up with Knight and another soldier, Lane, who have come under attack from the Yeti. When they try to detonate some explosives against the Yeti, the bombs fail to explode, the blast being smothered by the web generated by the Yeti guns. The Yeti retreat, leaving the soldiers and Jamie to escape. Elsewhere in the underground, the web is expanding once more, swamping Kings Cross and then moving on. It seems to be engulfing the whole of the Circle Line, entrapping central London.
Back at the base, Victoria has overheard Anne Travers speculating that she and the Doctor might be behind the Yeti emergence and so heads off alone to the tunnels to look for the Doctor. Elsewhere in the tunnels another soldier, Private Evans, is found; he is seemingly the only survivor from an attack by the Yeti. He explains that the fungus is being grown and stimulated by the use of a glass pyramid, which Jamie recalls was crucial to the Great Intelligence's development in Tibet. Evans agrees to accompany Jamie back into the tunnels, and it is only a matter of time before they become trapped by the expanding fungal web.
Egged on by Jamie, Evans destroys a pyramid of spheres carried by one of the Yeti and this enables them to make their escape.
Elsewhere in the tunnels the Doctor and Victoria are reunited. Professor Travers is overjoyed to see the Doctor again, offering to vouch for him, and together they start to examine Yeti control spheres. The Doctor is sure the Great Intelligence is attempting to conquer Earth once more, and has brought him here for some reason too. Travers is convinced he has brought the Intelligence back to Earth by running experiments on one of the spheres from Tibet and succeeding in activating it. The Doctor remarks that the Yeti seem to have been upgraded since their last encounter.
The personnel at the base are getting ever more nervous as they are entrapped. The fungus continues to spread, now consuming Chancery Lane. The Doctor advocates blowing up the tunnel just outside the Goodge Street station, thus sealing them in and away from the expanding web fungus. However, it now seems that there is an enemy in their midst: someone unbars the doors to the base and places a beacon for the Yeti in the explosives store. Soon a Yeti is advancing on the HQ and deposits a load of pulsating fungus inside the storeroom. It can be contained by closing the doors, but has wreaked damage by consuming all the explosives within and thus preventing the Doctor’s detonation plan. The Colonel decides that an alternative plan would be to get hold of explosives elsewhere. Jamie and Evans return to the base, which is attacked by a Yeti.
The Yeti knocks Travers out and drags him away. The fungus also attacks Captain Knight’s group and prevents them reaching the necessary explosives.
The Doctor retrieves some of the fungal web from the tunnels and decides to start experimenting on it. When he and his friends return to the base they find Anne unconscious and Travers gone. The Doctor begins to explain the nature and threat of the Great Intelligence. He also starts to examine the functioning of the control spheres, seeking to develop a control box. A little later, he and Knight venture out to the surface looking for transistors to build a control box, but the Yeti attack them and kill Knight but not the Doctor. It seems they were drawn to the Yeti model deposited in Knight’s pocket. The Doctor returns to HQ and reports the death to Anne, Jamie and Victoria, while Evans returns too, with news of a disastrous mission to try and retrieve the TARDIS from Covent Garden. The Yeti attacks again and kills more soldiers. Lethbridge-Stewart, the Commanding Officer, is the only survivor when he returns to HQ and meets the Doctor, Anne, Jamie and Evans. The Doctor works out that Lethbridge-Stewart is being tracked using a missing Yeti model and seconds later two Yeti burst in, accompanied by a haggard and distraught Professor Travers.
Travers is used as a conduit for the voice of the Great Intelligence, which is now controlling his body. The Great Intelligence explains that It brought the Doctor here in order to drain his mind. Unless he surrenders to the Intelligence, the entity will drain the brains of Jamie and Victoria. Victoria is taken as a hostage by Travers and the Yeti while the Doctor is given twenty minutes to ponder his future. He decides to surrender himself if he can’t find another solution and applies himself to the control box once more, succeeding in reanimating a broken control sphere. He and Anne manage to get the control box to direct the sphere if they are kept very close. The Doctor then develops a voice control system for the sphere.
Victoria is taken to Piccadilly Circus tube station where the Intelligence abandons Its control of Travers. They are soon joined by Staff Sergeant Arnold, who turns up dishevelled and bleeding, having somehow survived the web. He is hidden from the Yeti and agrees to head off to HQ to tell the Doctor what is happening. Arnold soon links up with the Colonel and Jamie, who are searching in the tunnels. All three agree to return to HQ to support the Doctor, but he and Anne have gone off to Warren Street to track down and seize a Yeti. They manage to overpower one and substitute the servile control sphere. Back at HQ things take a further turn for the worse when the fungal web bursts through the walls.
The Doctor and Anne release their servile Yeti, knowing it can be controlled later if needed, and then they run into Jamie and the Colonel who bring them up to speed with the situation. A little later they find Arnold, who explains that HQ has been destroyed and Evans has deserted. He slips away again while the others are herded by the Yeti and marched toward Piccadilly. In the central ticket hall of Piccadilly Station, there is an enormous glass pyramid, which is there to manifest the Yeti. The Doctor, Jamie, Victoria, Anne, Travers and Lethbridge-Stewart are all reunited at Piccadilly Circus, with Evans brought to them soon afterward. It turns out that the human agent of the Great Intelligence is Staff Sergeant Arnold, who has been killed and his body animated by the Intelligence. The Doctor is sent into the glass pyramid and is just about to have his mind drained when Jamie unmasks the servile Yeti and uses it in an assault. The pyramid is destroyed in the ensuing scuffle, detonating all the Yeti control spheres, and the corpse of Arnold falls dead. Everyone is happy except for the Doctor. He explains that he had sabotaged the conversion headset and would have drained the Intelligence if the device had been used – but now the Intelligence is free once more. The Doctor, Jamie and Victoria slip away and head back to the TARDIS in Covent Garden.