Tibet
During the life of Padmasambhava and Yeshe Tsogyal the presence of non-celibate and monastic practitioners grew in numbers in Tibet. After Padmasambhava's life-time, Buddhism and Buddhist teachings, though they were the state religion, were heavily suppressed under the reign of Tibetan King Langdarma during 836-842 c.e.. While monastaries carry big institutions of study, mass training, learning and record, the Yogins and Siddhas existed primarily outside of institutions. When monastic Buddhism underwent political persecution under the reign of Langdarma, it was actually the Yogic (non-monastic) practitioners who kept the teachings alive. The monastaries and monks were easy to eliminate by eliminating their institutions and anyone in monastic uniform. In contrast, the Yogic, non-monastic practitioners, who often wore conventional clothing, lived scattered amongs ordinary people, were much more difficult to locate and obliterate. The ensuing period of the 9th and 10th century, for which there is little historical record, was the time of Nyingma and Yongdrung Bon schools.

India
Meanwhile in India, Tantric teachings of various traditions were reaching their greatest height and widespread cultural infence. The MahaSiddha Tradition was being expressed fully and visibly in India by such masters as Tilopa (988 - 1069, Naropa (1016 - 1100) and Niguma (circa 1025). These MahaSiddhas had far reaching influence which spread to Tibet, but the MahaSiddhas hey-day in India was short lived. A series of brutal Turkish-Muslim conquests began in 1200's and eventually gained rulership over the Indian sub-continent from the 13th-16th century. Though a few rulers accomodated local traditions, generally there was violent suppression of Indian religious practices, including the Tantras. The biggest university and largest religious library in the world, Nalanda university, was destroyed and its texts burned. Under religious oppression in India, the MahaSiddha tradition all but dissappeared. Tibet, who eventually marganilized the tradition, became it's primary home though pockets of it continued in specific persons and within small lineages throughout the Himalayas. So the MahaSiddha Tradition continued to exist as a fringe phenomena that occassionaly emerged into historic visibility but remained largely invisible.

Secong Spread of Buddhism in Tibet
Despite the attempt to subdue Buddhism, around the 11th century, there was a second spread of buddhism throughout Tibet under a government sponsored revival of monastic Buddhism. A more varied influence of teachings, practices and translations of Indian Tantras come to Tibet. The country also came under the influence of the MahaSiddhas such as Machig Labdron, Marpa and Milarepa. A crystallization of various lineages, and establishment of new schools of Buddhism developed into Shangpa Kagyu (1057), Kagyu (1125), Shijed, Chod, Kadampa, Reformed Bon, and Shakya schools.

The Climate in Tibet became uncreasingly unwelcoming to the Yogic tradition of the MahaSiddhas and their Inner Tantras, but due to the flourishing of these practices in India, they could not be denied completely. Therefore, Vajrayana was modified and adapted into a form to be found exclusively in the monasteries. It was discouraged from being practiced outside the monastaries. Though Buddhism was sponsored as the national religion, the Buddhism recognized as such was exclusively Sutric Buddhism of the Monasteries and the monastic version of Vajrayana. The Vajrayana of the Monastaries was expressed primarily through the outer tantras to conform to Monastic codes of conduct. It was also portrayed as a stage in the sequential path through the yanas wherein one would practice the modified Vajrayana only after years of Sutric study. A far cry from the eccentricity of the MahaSiddhas who originally embodied these teachings, from this period on Vajrayana was expressed primarily in the style of sutra and the outer tantras. The Yogic tradition of the MahaSiddhas became outlawed, but individual Masters continued to privately teach their disciples without government sanction or sponorship. As per the Outer Tantras, the Vajrayana was expressed in long rituals and liturgies; and as per sutra, it was practiced primarily by men. Still today this Sutricized Vajrayana is widely considered the way to practice Vajrayana, as it if it were a homogenous, monastic tradition.

Many of the disciples of Padmasambhava and Yeshe Tsogyal were women, but within the second spread of the dharma the participation of women became less common until they gradually took an inferior role. Women practitioners and non-celibate practitioners were no longer politically or culturally accepted in the emerging new frame work of Tibetan Buddhism. Despite the modification and adaptaption of Vajrayana to the monastic institution in Tibet, the original tradition lived on privately in family lineages and in transmission from Root Teacher to Disciple as well as through the ever renewing terma tradition. The original impulse of the MahaSiddhas continues to this day, but to this day it remains rare and marginalized.

It is important for Yogic practitioners to remember that even though the monastic expression of Vajrayana became most widely known, it was not the original or only expression of the Tantric Buddhist path. Yogic, non-celibate lineages who practiced inner Tantras directly and non-elaborately still continued to exist, though they were increasingly marginalized.

In 1409, the Gelugpa school of Tibetan Buddhism (the Dalai Lama's monastic lineage) was established. In the 17th century, the Gelugpa tradition took political leadership over Tibet, beginning the tradition of the Dalai Lama. An ongoing cycle of political-religious struggle and sectarianism ensued and continued until China overtook Tibet in 1959. There was a general decline in the dharma, even though a few great masters continued to appear.