The sacred relics that were left behind by the cremation fire were placed inside eight types of stupas, which were all made of silver. These were then brought to Drepung Upper Residence but strange voices and squeezing sounds were heard to arise from the relics.

Following Nechung’s instructions, the Desi took the relics out of the stupas and placed them inside a wooden box that was then cast into the Kyichu River. It eventually came to rest in lower Lhoka Dol, which is known today as the White Spring of Dol.

The "spirit" of Tulku Drakpa Gyeltsen initially travelled to Tashi Lhumpo hoping to meet his Guru, Panchen Lobsang Chokyi Gyeltsen. However, the Horse Lords of Vaishravana, who stood encircling the monastery, barred access to the monastery.

The "spirit" then traveled to Sakya, led by imprints of his previous life as Sakya Pandita. The patriarch of Sakya at that time, Dagchen Dorje Chang Sonam Rinchen, recognised and enthroned him as a Dharma Protector and Kunkhyen Ngawang Kungo Lodroe then composed a praise to him. Dorje Shugden practice flourished henceforth in the Sakya School until recent times.

However, back in Lhasa, the calamities that had hit the capital continued to intensify. Even the Dalai Lama was affected – he beheld many inauspicious apparitions that seemed to plague and disturb him.

When the Dalai Lama gave an initiation, the initiation torma fell on its own accord without the slightest breeze. When he was served meals, the plates of food would overturn for no reason; he couldn’t even drink a cup of a tea without the teacup shaking from disturbances. One time, it even seemed that the entire Potala Palace was rocking back and forth.

The Dalai Lama sensed that all these occurrences were bad omens. "We have wronged Tulku Drakpa Gyeltsen," he said. "He has died and become a raging, evil spirit." The Dalai Lama resolved to destroy this spirit using tantric rituals. The first ritual, a wrathful fire puja, was performed by the 5th Dalai Lama himself. The ritual failed because the Dharma Protector Setrab manifested a miraculous monastery on top of the mountain, which rocked the Potala Palace; this distracted the Dalai Lama from his ritual and the "spirit" was freed.

The 5th Dalai Lama then contracted other very powerful tantric masters of the Nyingma tradition, such as Dordrag Rigtzin, Minling Terchen and Gadong Ngarampa, to perform similarly deadly rituals to destroy the "spirit" of Tulku Drakpa Gyeltsen.

However, all of them failed too as Setrab would manifest more distractions to pull the Lamas' attention away; or when they were able to attract the spirit onto the ritual ladle, to be burned in the fire puja, they were unable to destroy him in the fire. Whenever the Nyingma Lamas dipped the ladle into the fire, an indestructible image of Yamantaka would arise instead, and stand atop the ladle.

Such magical incidents revealed the true nature of Tulku Drakpa Gyeltsen, which is that he is one with Yamantaka, the wrathful emanation of Manjushri, Buddha of Wisdom. The nature of Yamantaka is beyond death and rebirth, as he is fully enlightened. This was why neither the Dalai Lama nor Nyingma Lamas were able to destroy this "spirit".