Following the parinirvana of her root teacher and father, Chögyal Ogyen Terdag Lingpa, Jetsün Migyur Paldrön remained mainly in retreat. However in 1718, as prophesized by Guru Padmasambhava, the Dzungar Mongols invaded and thereby ended her retreat. This invasion brought great destruction throughout Tibet and was particularly detrimental to the precious doctrine as monasteries were destroyed and the lives of an immeasurable number of dharma practitioners were lost.
According to the recorded sources of that time, "A great number of the army under the Dzungar Mongol General, Ju Ring Thu Hong Tha'i Ji, filled the slopes of Tibet. The very name of the doctrine of the great secret mantrayana was crushed, temples destroyed, many great monasteries were razed to the ground and practitioners were scattered all across fleeing for their lives. The great Land of Snow-clad Mountains, having been thus far blessed by great masters such as Padmasambhava, great panditas, dharma kings, translators, mahasiddhas and learned ones such as the All-Knowing Terdag Lingpa, had become equal to the realm of Padmasambhava's buddha field (rnga yab pad ma 'od). But the Land of Snow was now filled with darkness pervading in all directions, resembling twilight without a lamp."
One year after the beginning of the Mongol invasion, in the Earth Dog Year (1718), Lochen Dharmashri and Pema Gyurme Gyatso, Jetsün Migyur Paldrön's uncle and elder brother respectively, were summoned to Lhasa and held captive. Shortly after, the invading army began entering monasteries in Central Tibet including Mindrolling and Dorje Drak, setting fire to the temples, completely destroying everything in their path and imprisoning or killing monks, nuns and practitioners. It was only three to five years after the completion of the great Mindrolling Monastery, established by Ogyen Terdag Lingpa, that it was completely destroyed by the invading forces of Dzungar Mongols (see previous section on Dzungar Mongol Invasion).
Fearing for the only remaining members of the lineage, the elder monks and attendants who had managed to elude capture requested Jetsün Migyur Paldrön to leave immediately. Enquiring after her brother, Drinchen Rinchen Namgyal, her mother, Yum Phunstog Plazom and sisters, she was informed that that they all had fled, assisted by their attendants. However, there had been no news as to whether or not they had been successful in their escape.
She went to the private shrine of the residence and offered prayers. She then took the little statue of her revered father, Terdag Lingpa, and storing it safely in her backpack she prepared to leave Mindrolling. That evening, wearing a simple woolen dress and her hair, which had grown while in retreat, tied in a scarf, Jetsün Migyur Paldrön disguised herself as a lay person. Accompanied by a few trusted attendants, Gyurme Chödrön, her cook Gyurme Yangzom, Gelong Tashi Wangchuk and Gedün Tshamphel, they made their escape through a secret door over the peak which was behind the statue of Terdag Lingpa.
Terdag Lingpa in his lifetime had told his daughter, Jetsün Migyur Paldrön, to have a small backdoor built leading out of her living quarters to the back hills of Mindrolling. Backdoors were not so common in Tibet during that time but Jetsün Migyur Paldrön followed the command of her father and had the door built as he wished. When Jetsün Migyur Paldrön asked Terdag Lingpa about it, he told her that someday it would be of great benefit to her.
While Jetsün Migyur Paldrön was making her escape, the Dzungar Mongol army razed the monastery. The main temple, Chökhor Lhunpo (the main residence), the great stupa, and all the quarters of the monks were destroyed, leaving only Sang Ngag Phodrang (one of the main temples). The powerful army wrought such havoc and left the entire area of Drachi so desolate that, to this day, the area around Drachi has never fully recovered from the destruction.
During this same time, Sangyum Phunstog Palzom and Semo Palzin, Jetsün Migyur Paldrön's mother and sister respectively, were captured by the Mongol army. While being harassed and interrogated by the Mongols, Sangyum Phunstog Palzom was unable to contain herself and blurted out "I have a daughter, the great lady, Migyur Paldrön. Like a great dragon she will ensure that you are not successful in your evil actions." The General, realizing that Jetsün Migyur Paldrön was still alive, sent out troops to search for her. The early records say, 'in the whole valley, every pass, in every corner of the land, the cry of the Mongols resounded.' To ensure that the army understood the importance it placed on finding Jetsün Migyur Paldrön, the General decreed, "If Terdag Lingpa's daughter is not caught and brought here, your necks will be on the line. Day or night, she must be captured and brought to me."
Fleeing from Mindrolling, Jetsün Migyur Paldrön and her attendants reached the home of Depa Wangdu at Tsamyul. However, they had barely arrived when the troops searching for them descended on his home. Cleverly stalling them with offerings of beer, Depa Wangdu gave Jetsün Migyur Paldrön and her attendants the time they needed to make a quick escape by sliding down a rope tied under a small window of the house. They hid in a narrow space behind a mass of slate rocks, at the head of a long valley, while the horsemen roamed back and forth above their heads searching for them.
They remained in hiding for two full days. In one of her biographies, Jetsün Migyur Paldrön recounted the days saying, ""My heart was pounding with terror. I thought we would be captured but due to the blessings of the Three Jewels in general and in particular, the Glorious Guru of Orgyen, we remained safe." The Mongols, unable to find her, finally left to search in another direction and Jetsün Migyur Paldrön and her party left for sman brjid (Menjid).
Her attendants and the senior monks at Menjid, such as Drön Nyer Powo (gnyerpa spo bo), Bum Rabjampa ('bum rab 'byams pa), Orgyen Kelzang (o rgyan skal bzang), Shabdrung Gyurme Shenphen Wangpo ('gyur med gzhan phan dbang po), Gelong Ogyen Rabten (dge slong o rgyan rab rtan) and others, consulted together saying "the quintessence of Terdag Lingpa is in this child. We must ensure that she is safe. We must serve together so that the monastic body of the lineage can gather once again and be re-established." They decided that they would all scatter in different directions so that in the event of being captured, at least someone would survive to serve the lineage. Gelong Ogyen Rabten took the responsibility of leading Jetsün Migyur Paldrön and her attendants to safety and decided to head to Sikkim via Phagri.
Having just been in a strict retreat and being accustomed to travelling on horseback instead of by foot, the journey through rough terrain for days and nights without respite took its toll on Jetsün Migyur Paldrön and she fell ill. The heat and exhaustion also affected the entourage and upon reaching Phagri they stopped for rest. Gedün Tshamphel ventured into the little town market only to return hurriedly with the news that in the market, two horsemen had arrived with a notice saying 'Terdag Lingpa's daughter must be found and caught immediately. The People of Phari must not allow her to escape and they must inform the army officials if they see her.' Hearing this, although exhausted and ill, they left immediately taking the most narrow and precipitous path into Sikkim. Gelong Tashi Wangchuk and Gedün Tshamphel having previously travelled to Sikkim were fortunately able to find the way.
As the travelling party reached the border of Sikkim, a man carrying news from Lhasa arrived. They told Jetsün Migyur Paldrön of the assassination of her uncle, the great Lochen Dharmashri, and her elder brother Pema Gyurme Gyatso (see the biographical accounts of Lochen Dharmashri and Pema Gyurme Gyatso). Her other elder brother, Zhabdrung Yidzhin Legdrup, her uncle, Ahku Chagdzöd, and all the senior lopöns and umdzes that remained at Mindrolling had also been killed. The message also contained a warning for her to be careful.
Struck with immeasurable grief and with tears in her eyes, Jetsün Migyur Paldrön turned towards Lhasa and with folded hands supplicated to the guru. Thus, calling the guru from afar, she then saw the figures of Guru Rinpoche, Yeshe Tsogyal and Terdag Lingpa. Appearing in the sky in an array of rainbows, they blessed her and assuaged her grief and gave her clear instructions for the future.
Shortly after this, the party safely reached their destination and temporary refuge- Sikkim. Thereafter, the King of Sikkim and Dzogchen Thrakthung Pawo Jigme Dorje, upon hearing of the arrival of the great dakini Jetsün Migyur Paldrön, arranged a grand welcome with a golden procession leading her to the golden throne. The next day Jetsün Migyur Paldrön once again shaved her head and donned the robes of a nun.
Thereafter the King made an unprecedented proclamation, (without the permission of the King or the great Dzogchenpa, people were not allowed to receive teachings from anyone in an attempt to reduce charlatans from misleading people) which he had never made for any previous lama. The King proclaimed, "All people of Sikkim, lay or clergy, behold how very fortunate we are. The daughter of the Root Guru, Tamer of Beings, Terdag Lingpa, and herself the unmistaken emanation of Yeshe Tsogyal, Jetsün Migyur Paldrön, has blessed our kingdom with her presence. All fortunate ones, who wish to request empowerments, dharma transmissions and so forth, can now do so without hindrance or restraint."
Over four thousand practitioners gathered for several months while Jetsün Migyur Paldrön bestowed many empowerments and teachings. Upon Dzogchen Thrakthung Pawo Jigme Dorje, the King, a few principle attendants and fortunate students, she conferred the entirety of Terdag Lingpa's new termas and in particular the empowerments and commentary of Ati, her own cycle of teachings (giving it for the first time) as well as many new and old terma teachings and empowerments. It is said that during this period there were many wondrous signs including a rainbow settling over the mandala and the great Jetsünma. It was in this way that she became the root teacher of the King of Sikkim and countless practitioners of Sikkim and how she established the banner of the Dzogchen teachings throughout this region. In turn, the great Dzogchenpa bestowed upon Jetsün Migyur Paldrön the Könchog Kyidu (dkon mchog spyi 'dus) and Rigzin Sogdrub (rig 'dzin srog sgrub) empowerments and transmissions. Due to this, a strong connection has always existed between the dharma practitioners of Sikkim and the Mindrolling lineage. The monastery and the many sacred places where Jetsünma transmitted the teaching are still present in Sikkim and continue to hold her teachings and lineage to this day.
It was during this time, of Jetsün Migyur Paldrön's great activities in Sikkim that her mother and sisters, Semo Paldzin and Semo Buga Kyidzom, managed to escape the perils in Tibet and join her in Sikkim. This was an incredibly joyful reunion for mother, daughter and sisters. However, soon the news of Jetsün Migyur Paldrön's escape into Sikkim reached Lhasa and the ears of Lord Tsering Dhöndup who was the commander of the Mongolian troops stationed there. He immediately sent his most skilled horsemen with a guide to Sikkim in an attempt to capture Jetsün Migyur Paldrön and bring her back to Lhasa.
Recalling the instructions she had received from Terdag Lingpa, Jetsün Migyur Paldrön and the great master Dzogchenpa performed the wrathful practice of subjugating the evil forces. Within a few days of these practices, a great disagreement arose among the Mongolian army that created intense internal conflict. The weather also suddenly changed drastically, bringing several weeks of harsh snowstorms, the likes of which had never been seen before, causing the army camp to be completely destroyed.
In Lhasa the Dzungar Mongolian army was not faring any better. Their power had weakened greatly due to inner conflicts and various other difficulties. Many of their generals had been forced to flee. It was only a matter of time before the army was defeated and the occupation by the Dzungar Mongols in Tibet came to an end.
Upon hearing of the defeat of the Dzungar Mongols, Jetsün Migyur Paldrön and her entourage began preparing for their return to Tibet. It is said that one of her surviving sisters remained in Sikkim and married the Chögyal, the King of Sikkim. Upon hearing the news of her departure, the king and thousands of heart-sons and daughters of Jetsün Migyur Paldrön formed a farewell procession with heavy hearts. They accompanied her to the border of Tibet and stood watching as she entered back into Tibet.
The party travelled to Tibet by crossing Phagri and Kharola through the ba bcos pass and making a stop at the estate of her maternal unlce, Dumpowa, who was overjoyed to see her again. During her stay, Jetsün Migyur Paldrön conferred the Red Guru Drakpo (Drakmar) and long-life empowerment on her uncle, all the surviving members of the family, the retainers and all those fortunate to be there. In the records it is said that during one of her public addresses she stated, "It feels like I have returned from the bardo."
Shortly after conferring the empowerments Jetsün Migyur Paldrön arrived in Dargye Chöling in Central Tibet. She bestwoed countless empowerments, teachings and audiences to the public, and, like a wish fulfilling jewel, completely fulfilled the wishes of everyone who approached her.
The morning after her arrival in Dargye Chöling, Orgyen Rabga (o rgyan rab dga'), who had been the chöpön of Terdag Lingpa, came to offer her a khatag (white scarf). He also offered her two chests of precious objects used in empowerments that had belonged to Terdag Lingpa. Amazed that these blessed and precious items had been saved from destruction, and delighted by this auspicious tendrel, Jetsün Migyur Paldrön felt renewed strength and courage to set out for Mindrolling.