At some point in the 1600s, Padmasambhava - the master of Detsen, a monastery in the Tibetan Himalayas - was on an astral-projection journey when, in the depths of space, he encountered a formless entity. The Great Intelligence, as it called itself, told Padmasambhava that it wanted to have a form again, and that it would inhabit only a small part of the mountain on which Detsen monastery was located. Ignorant of the Great Intelligence's true purpose, Padmasambhava allowed it to pursue its experiment, and from that point forward, the Great Intelligence used Padmasambhava's mind and controlled his body.
The Great Intelligence kept Padmasambhava alive for three hundred years serving its cause. For the first two hundred of those years, Padmasambhava - presumably with the help of his abbot, Songsten, who was also under the Intelligence's control; and probably also using the telekinetic powers which the Great Intelligence possesses - built several Yeti and control units, as well as a cave in the mountainside where the Intelligence could exist in its corporeal form. Because Padmasambhava was also kept in isolation in the monastery's inner sanctum, he was able to build a control room behind his throne, in which the controller for all the Yeti was located. Padmasambhava and Songsten keep any of the monks from becoming suspicious by telling them to forget anything they should not have seen, and in this way their memories are wiped.
The Yeti are designed to look like the actual Yeti that inhabit the Himalayas (although these creatures are slighter of build and more timid than the Yeti built by the Intelligence). They are not organic at all - they are actually robots, made of metal, that cannot be hurt by gunfire or any other kind of weapon (although they dislike fire and are enraged by Galactic Glitters). They are very strong, and despite their outwardly cuddly appearance, one slash of their vicious claws can end a man's life.
The Yeti are powered by a control unit - a small silver sphere which fits neatly into a cavity in their chest, covered by a flap of fur. These spheres, filled with circuitry, are programmed to return to their Yeti, and can move on their own in order to do so. This can be stopped by plugging the hole in the Yeti's chest with something else, like a rock; apparently this fools the control unit into believing it is no longer needed. The control units enable the Great Intelligence to direct the movements of the Yeti, so that they remain immobile, unable to see or feel anything, until they are activated for service, at which point they jerk into life and begin lumbering around to do the Intelligence's tasks. The control units bleep when the Yeti are active, or when they are moving under their own power. The control units can also be rewired so that they obey voice commands given by someone other than the Great Intelligence, and the signals sent to control the Yeti can also be jammed. The Intelligence uses small Yeti pawns as a means of directing them, usually by moving them around on a map of the local area, but the pawns can also be used as homing beacons, placed in locations which the Intelligence wants the Yeti to attack.
In Tibet, the Intelligence's Great Plan is not simply to become corporeal and inhabit one small cave in one mountain; it breaks its agreement with Padmasambhava and demands the entire mountain. Padmasambhava soon realizes that the Intelligence will not be satisfied with the mountain, either; it will go on to engulf the world. But by this point, it is too late. The Great Intelligence has put a small glowing pyramid of spheres inside the cave. Later it has these arranged into an intricate pattern, with a glass pyramid placed at the center. The power of the Intelligence grows until it can take on a physical form - and it does this by cracking the pyramid, which releases the Intelligence in the form of a sludge, accompanied by a blinding white light and a piercing noise.
Jamie is able to stop the Intelligence by smashing the large sphere inside its control room. With this done, the control units in the Yeti explode, disabling them. Jamie then smashes a large glass pyramid in the control room, which causes the pyramid in the cave to explode and take part of the mountain with it. This severs the Great Intelligence's link with Earth, giving Padmasambhava back his body - and finally, after living for over three hundred years, he can die. Professor Travers, an English anthropologist who was searching for the Yeti, then spots a real one lurking on the mountainside and goes after it.
Upon returning to England after his adventure, Travers takes with him one of the Yeti, as well as a control sphere and several of the small Yeti models. He sells the Yeti to a local museum, and tinkers with the control sphere, curious to see if he can bring it back to life. About thirty years later, he finally succeeds - but the Intelligence homes in on the control sphere, which then disappears from his lab and finds its way back to the Yeti in the museum. Now that the Intelligence has a pair of hands in its service, it instructs the Yeti to build more. These new Yeti are somewhat different from the previous versions - their eyes glow when they are active, they roar, and they carry web guns that fire a web which kills on contact.
London first notices something awry when the streets are covered in a blanketing mist, different from the usual London fog in that it does not go away, it absorbs radio waves, and the people who walk into it never walk out. Two days after the appearance of the mist, a pulsating white weblike fungus begins to grow in the Underground. It extends above and below the tunnels through which it is spreading, and although a respirator provides temporary protection for anyone trying to penetrate it, these are easily pulled off, and death is almost certain for anyone entering it. Then, two days after the first fungus sighting, the Yeti make their first appearances in London. They destroy all the telephone lines, and kill people with their web guns, causing London to be completely evacuated.
Since its first meeting with the Doctor, the Great Intelligence has been watching him, and has come to the conclusion that his is the greatest mind that the Intelligence has seen. It traps the TARDIS using some of the weblike fungus, and then releases it so that the Doctor lands in the middle of the Underground. The Intelligence has invented a machine, a ten-foot glass pyramid with a seat inside, which will drain all the Doctor's knowledge and past experiences from his mind, and allow the Great Intelligence to absorb them. But the Doctor is able to reverse the wiring in the helmet that the Intelligence places on him, so that instead of the Intelligence draining him, he can drain the Intelligence. Unfortunately, before the Intelligence can begin the mind-draining process, Jamie and Victoria manage to pull him out of the machine and blow it up, destroying the Yeti's control units in the process. Instead of destroying the Intelligence forever, its ties with Earth are merely severed again...giving it another opportunity to attack in the future.