During this initial heyday, the Nyingma tradition was the whole of Tibetan Buddhism. In the middle of the 9th century however, Buddhism was persecuted by King Lang Darma (r. 836-842), who took the throne after the assassination of the Dharma king Tri Relwajen. When Lang Darma in turn was assassinated by a Buddhist adept, Lhalung Pelgyi Dorje, the Yarlung dynasty was thrown into chaos, and the country soon split into poorly coordinated regions. Buddhist monks fled to the outer provinces. The recently translated Buddhist texts were destroyed or hidden. The Buddhist temples and monasteries were unable to function for a long time.
From the middle of the 10th century, the Dharma began to return to the central regions. At the same time, later forms of Indian Buddhism entered Tibet through the work of numerous Tibetan translators and Indian masters. Around this time, the Nyingma was formed into a distinctive order; it was based on the spiritual lineages preserved in the families of the descendants of the disciples of Padmasambhava, on the sacred texts in the "old" translations done in the Samye period, and on the monastic traditions descended from Shantarakshita.
During the period of the later waves, the Nyingma traditions were collected and preserved by many scholars, although because of its relative paucity of monasteries the order remained a minority movement. Then, in the 14th century, it too caught the monastery fever and built six major centers around Tibet. The greatest of its lamas in this period was the incomparable Longchen Rapjam Tsultim Lodro, considered a direct incarnation of the Bodhisattva Manjushri. He synthesized the whole Buddhist teaching into a systematic path leading up to the Great Perfection. His numerous works are among Tibet's greatest treasures and have served as the foundation and summit of the Nyingma curriculum until the present day.
This description by Dr. Shailendra Kumar Verma, Ph.D. His doctorate thesis being on the "Emergence and Evolution of the Buddha Image (from its inception to 8th century A.D).