Professor Travers, an anthropologist and explorer, is awoken from his sleep when he hears the screams of his companion. He is horrified to see a lumbering, hairy creature standing over his friend's lifeless body. The beast grabs Travers's gun and twists it into scrap metal as the terrified man scampers into the night.
The TARDIS has materialised on a cold and windy hillside. Inside, the Doctor is delighted at their destination and tells his companions Jamie and Victoria to start searching for what he calls a 'Holy Ghanta'. When Jamie inquires where they are, the Doctor reveals they have landed in Tibet, and that the Detsen Monastery will "give them a welcome of a lifetime" if they arrive with the Ghanta: a bell and holy Buddhist relic which the Doctor took some three hundred years ago for safe-keeping.
While the Doctor steps outside to investigate (dressed in an extremely furry coat), Jamie and Victoria locate the Ghanta along with an impressive looking sword which Jamie decides to keep. Meanwhile the Doctor is certain he is being watched and elects to travel to the monastery first to prepare the way. En route, he finds the remains of Travers's camp and the dead body. He takes the rucksack with him as evidence.
Victoria quickly gets bored of being stuck in the TARDIS and convinces Jamie to explore. Jamie is convinced that as a highlander he will be unaffected by the harsh chill, but he soon discovers otherwise. They soon discover huge animal footprints that encircle the TARDIS.
The Doctor arrives at the monastery, clutching the remains of Travers's rifle and rucksack, but there is no response when he knocks on the large wooden doors. The inner courtyard is strangely deserted. However, when he turns back to the door, his route is blocked by a group of armed monks. Travers is also present and before the Doctor can explain his presence, he spots his rucksack in the Doctor's hand. Travers is convinced that the Doctor must be responsible for the death of his friend, despite his earlier claims to the monks that a "beast" had done so.
The Doctor loudly protests his innocence to the peaceful monks, but Travers is determined that he is lying. The leading Warrior Monk, a gruff man by the name of Khrisong, states that this matter would be of little consequence had some of their own not also been killed. The Doctor is thrown into a cell to await the monks' decision. Khrisong is not sure of Travers or why the stranger has come to the monastery.
Back on the hillside, Jamie and Victoria have been following the trails of footprints right to the mouth of a deep cave. Jamie at first is not willing to enter it for fear of some savage animal, but he changes his mind when he spots timbers holding up the roof. Victoria spots a huge creature at the cave mouth, and the pair watch in horror as massive claws push a boulder which traps them inside.
The Doctor is increasingly irritated within the confines of his cell and climbs up to a small window in order to peer outside. Travers pops his head through a hatch and mockingly informs him of the hundred foot drop beneath the window. He goes on to accuse the Doctor of being a sabotaging journalist.
When the Doctor asks what Travers is talking about, Travers cries, "You know! The Yeti! The Abominable Snowmen!"
The Doctor's response is simple enough – he knows from experience that the Yeti are naturally timid, so they aren't the culprits. And he certainly does not have the strength of the beasts himself, for all his fur. Travers simply states that "Khrisong will find out the truth".
Indeed, the Warrior monk is in conference within the courtyard over the fate of this apparent murderer. The other monks doubt whether Travers can be certain of his claims, but Khrisong is less sure. "He is an Englishman. Why should he lie?" The monks respond by saying they were almost certain the Yeti were in some way responsible. Khrisong states that this odd shift in behaviour makes the stranger still more threatening – he therefore requests a chance to prove the Doctor's guilt. The monks recoil in horror: "You are asking us to condemn a man to death." The warrior monk states he only does this to protect the others, his responsibility as Chief Warrior. But the more peaceful monks elect to turn over the whole matter to the Abbot following prayer. Once they have gone, Khrisong ignores their decision and orders for the Doctor to be brought to him.
Back in the darkness of the sealed cave, Jamie has discovered a pyramid of small silver spheres placed on a raised plinth. Before either can ponder their significance, the boulder shifts once more and the lumbering form of a Yeti enters the cave, trapping the pair of terrified travelers. Victoria screams as Jamie tries to defend her from the monster with his sword, only to see it snapped in two by the creature's hands as it lumbers toward them....
Jamie and Victoria evade the Yeti and depart with one of the strange illuminated spheres. They head toward the monastery, where the Doctor is still being detained on Khrisong’s orders. He has, nevertheless, been able to pass on the Ghanta to the friendly monk Thonmi. This novice takes it to the private chamber of Abbot Songsten, who is in communion with the master of the monastery, Padmasambhava. The ancient spiritual guide of the monastery knows the Doctor personally from his previous visit, and though he knows of the Doctor’s wisdom, he fears he will intervene in The Great Plan. Thonmi is told depart, his memory wiped of what he has heard, though left with the instruction of the Abbot that the Doctor should be released without harm.
The Doctor has meanwhile been placed on trial and, as a test of whether he controls the Yeti, is tied to the doors of the monastery as a means to lure the Yeti out. Travers has by now met Jamie and Victoria, who convince him the Doctor is no threat. The trio return to the monastery in time to see the Doctor freed on the Abbot’s instructions. Shortly afterward, the Yeti advance in an abortive attack on the monastery, during which one of them is overpowered and rendered dormant. The Doctor examines the captured creature and deduces it is some kind of robot, controlled by a missing spherical unit from its chest cavity. Elsewhere in the monastery, the sphere brought back by Jamie comes to life.
Travers has now become worried that the real Yeti are under threat from the robot ones, but some of the others now suspect he is the one controlling the robots. Outside the monastery he observes two of the robots come to life and head for Detsen. It soon appears the creatures are under the control of Padmasambhava, who is moving miniature Yeti like chess pieces around a map of the area. Inside the monastery the sphere slowly makes its way toward the dormant Yeti robot with the Doctor and monks looking for it, having worked out its purpose. Khrisong finds a sphere outside the walls of Detsen and the others observe the two Yeti retrieving it without harming it, leaving the Doctor to conclude that the two were obeying specific orders. Khrisong is now so overawed by the situation he begins to put his trust in the Doctor, who decides to try and return to the TARDIS with Jamie to get equipment to track the missing sphere. The pulsing globe finally reaches the dormant Yeti and revives it, causing the robot to menace Victoria and her new friend Thonmi.
The awakened Yeti battles its way out of Detsen, killing warrior monks in its wake, and leaving Khrisong angry that Thonmi opened the door to allow it to flee – albeit to avoid further bloodshed. Victoria and Thonmi are imprisoned for supposedly reviving the creature. The freed Yeti takes the sphere to the cave on the mountain, unaware it has been observed by Travers. Songsten himself soon arrives, guarded by Yeti, and bearing a glowing pyramid of spheres. The party deposits the pyramid in the cave and then departs. Travers sneaks into the cave and finds the pyramid pulsing with life, cracking open and oozing a strange cobweb substance. He flees in terror and makes back for the monastery, following the same path taken by Songesten, who is also returning to Detsen. The Abbot soon reports to Padmasambhava their plan is working and the old master replies that the Great Intelligence is thus already taking on corporeal form. To make way for the next phase, Padmasambhava orders, all monks must leave the monastery. This order is relayed throughout Detsen, though Khrisong is furious at such a command and is resistant.
When the Doctor and Jamie reach the TARDIS they find it guarded by another Yeti, but it is inactive and the Doctor takes out its control sphere for examination. He gets a tracking device from the TARDIS but moments later, in response to the pyramid, the sphere comes to life. It is only prevented from re-entering the dormant Yeti when Jamie lodges a rock in the open chest cavity. They too head back to the monastery but the sphere they have allows them to be pinpointed by their enemies and five Yeti are sent to deal with them. They only escape by giving up their sphere. When they return to the monastery the Doctor forges a new uneasy alliance with Khrisong based on the need to enable the monks to stay at the monastery. Realising the monks will not leave peacefully, Songsten opens the gates of the monastery to more Yeti.
Victoria has meanwhile given her jailers the slip and ventured alone to the Inner Sanctum of the monastery where, against all the commands, she witnesses the ancient and wizened face of the Master Padmasambhava.
Victoria soon realises the ancient man manipulating the small Yeti figures is commanding the robots around the countryside. He wipes her mind of their meeting and summons more Yeti to attack. In another part of the monastery Travers has returned from the mountain, but is delirious and incoherent in his ramblings about the glowing pyramid and a great evil that threatens them all. On command the Yeti retreat from the monastery once more, killing a monk named Rinchen before they depart. Even Khrisong now decides the monks must depart. Padmasambhava only wished to scare the monks away, not kill them all, and he sends Victoria as his emissary, speaking with his voice, to urge them to leave and not to blame the strangers, who are innocent of any evil. When the Doctor discovers Padmasambhava is still alive after three hundred years he becomes ever more concerned. He heads to the Inner Sanctum and confronts his old friend there. Padmasambhava explains that he encountered the formless Great Intelligence on the astral plane and the entity borrowed his form in order to conduct an experiment. It is an experiment that is now out of control and the old man seemingly passes away, lamenting his part in the situation. Seconds later the body of Padmasambhava is reanimated by the Great Intelligence, but the Doctor has returned to his friends and does not know this. The Doctor now helps Victoria recover from her trance-like state and then turns to help Travers, who is recovering his senses and explains about the cave and the pyramid. The Doctor pieces together the nature of the threat while Travers recalls that Songsten was in the cave too. It is clear Songsten is the link between the Yeti and the monastery. At the cave, the physical manifestation of the Intelligence is growing ever stronger and pouring forth menacingly.
In the Inner Sanctum Songsten has bowed totally to the will of the Great Intelligence, despite the voice of Padmasambhava lamenting the great evil, and slays Khrisong when the warrior monk arrives there. The Doctor and his friends arrive and overpower Songsten, realising he too has been entranced to commit the will of the Intelligence. Songsten is bound and returned to the other monks and the violence of his manner persuades them that he is indeed the threat to Detsen. The Doctor tells all the monks to flee quickly so that he can defeat the Intelligence, and he keeps Jamie, Victoria and Thonmi at his side while the others flee. He plans to destroy the equipment which the Intelligence is using through Padmasambhava to control the robotic Yeti, no more than minions in its quest for manifestation and domination. They venture to the Inner Sanctum once more where the Doctor distracts the being while Thonmi and Jamie start to destroy the equipment used to relay instructions to the Yeti. Some Yeti still attack the Sanctum, controlled by spheres, and it is not until these are destroyed that the robots become dormant once more. Destroying a further pyramid of spheres expels the Intelligence and, left in peace, the aged Padmasambhava finally dies, finding peace in the Doctor's arms. With the danger over, the travelers depart the ruined monastery. Travers accompanies them up the mountain and his belief in the real Yeti is renewed when he spots one on the moment. He charges off to investigate as the TARDIS departs.