At the age of thirteen Khyungpo Neljor studied Bon with Yungdrung Gyelwa (g.yung drung rgyal ba), and soon after studied Dzogchen with Jungne Sengge ('byung gnas seng ge), supposedly accumulating seven hundred disciples. He also studied with Kong / Kor Nirupa (kong / skor nu ru pa) in Shamora (sha mo ra) in Tolung (stod lung). According to Tsuklak Trengwa (gtsug lag 'phreng pa, 1504-1564/66), Nirupa taught him the Amanasei Chokor Nyernga (a mA na sa'i chos skor nyer lnga), a Dzogchen cycle allegedly invented by Sheuton Jang (she'u ston byang).
Not satisfied with the available teachings in Tibet, Khyungpo Neljor traveled to Nepal where he studied with a number of teachers. He served as an attendant of Amogavajra, also called Ratnakaragupta and Sauripa, and received teachings from him. From Vasumati he received inititation in the Kriya and Yoga tantras. He also studied with the ḍākinī of Devikoti, Kanashri; Ratnapela; and three disciples of Maitripa: Ratnavajra, Ksetravajra, Atulyavajra. According to the Blue Annals he also met Vairocana and received teachings from him.
After a short return to Tibet, Khyungpo Neljor traveled again to Nepal and on to India, where he studied with Danaśīla, a disciple of Nāropa. Having brought with him a considerable amount of gold, he offered it to numerous teachers in exchange for their instructions and transmissions. He met Maitripa, and received from him a teaching on White Mahākāla.
According to the Blue Annals, Khyungpo Neljor asked his teachers whether anyone in India had met the Buddha Vajradhāra, the source of the Buddhist tantras. They replied that Niguma, reputedly the sister of Nāropa, had done so. Khyungpo Neljor sought her out, finding her in the Sosa charnal ground in East India. He requested her transmission, to which she replied “I am a flesh-eating ḍākinī!” When he pressed her, she demanded gold. Taking his gold and throwing it into the forest, her retinue of ḍākinī formed a maṇḍala, bestowing on Khyungpo Naljor the initiation of the Illusory Body (sgyu lus) and Dream Yoga, two sections that make up the Nigu Chodruk (ni gu chos drug), or Six Yogas of Niguma. Niguma then transported him to a golden mountain summit where she bestowed the complete Six Yogas, the Dorje Tsikang (rdo rje tshig rkang) and the Gyuma Lamrim (sgyu ma lam rim). She prophesied that the teachings should stay secret until the seventh lineage holder, she being the second after Vajradhāra.
The list of additional teachers Khyungpo Neljor studied with includes the ḍākinī Sukhasiddi, a disciple of Virūpa who promised to manifest to his lineage; Rahulaguptavajra; Kamalarakṣita; and Atulyavajra. He returned to Tibet briefly to procure more gold, and then again to India to receive more teachings. Khyungpo Neljor reported that he met Atiśa Dīpaṃkara (c.982-1054) while passing through Toling on his return to Tibet, and compared texts that he had collected with those of Atiśa. Atiśa told him that his texts were authentic, and he suggested that Rinchen Zangpo (rin chen bzang po, 958-1055) and Dharma Lodro (dhar+ma blo gros) translate them. Given that Atiśa passed away in 1055, such an encounter is an historical impossibility, unless one was to accept that Khyungpo Neljor did indeed live for one hundred and fifty years, and if this incident took place during his youth.
Khyungpo Neljor received monastic ordination under the renowned Kadampa (bka' gdams pa) preceptor Langri Tangpa Dorje Sengge (glang ri thang pa rdo rje seng ge), the founder of Langtang (glang thang) monastery. He is reputed to have founded one hundred and eight monasteries in Tibet, although only two are known: Chakar ('chad dkar) in Penyul ('phen yul), and Zhangzhong Dorjeden (gzhang gzhong rdo rje gdan) in the Shang valley, in the year 1121.
The Blue Annals contains an interesting passage that suggests Khyungpo Neljor faced a certain amount of resistance to his teaching. Khyungpo Neljor accused “the monks” of focusing too much on books, and conjured apparitions of various peaceful and wrathful deities to propelled them to practice. However, jealous monks took up arms and Khyungpo Neljor had to conjure phantom troops to defeat them. He then went on to subjugate numerous non-human entities who were obstructing his teaching.
Khyungpo Neljor is said to have had six main disciples: Meuton (rme'u ston), Yorpo Gyamoche (g.yor po rgya mo che), Ngulton Rinwang (rngul ston rin dbang), Latopa Konchok Kar (la stod pa dkon mchog mkhar), Zhanggom Choseng (zhang sgom chos seng), and Mokchokpa Rinchen Tsondru (rmog lcog pa rin chen brtson 'grus). Only to Mokchokpa did Khyungpo Neljor transmit the entire Nigu Chodruk. Mokchokpa studied with Khyungpo Neljor for five years, until he was twenty-one, and returned to him some five years later to be with the master for the last year and a half of Khyungpo Neljor's life.
Khyungpo Neljor died in 1127. He requested that his body be preserved in a stupa, but certain Khampa disciples chose instead to cremate him, his ashes reportedly giving up numerous relics.
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