Phajo Drugom Shigpo originally hailed from Tibet. He studied the mysteries of the Drukpa school under Onre Darma Senge (1177-1237), the nephew of the eminent Tibetan master Tsangpa Gyare, at the remote monastery of Ralung in west-central Tibet. Phajo's children were all born after he arrived in Bhutan. Their descendants became prominent members of noted Buddhist lineages, such as the Changangkha Shelgno family, who founded the Changangkha Lhakhang. One of Phajo's other descendants, Dampa, also resided in the Thimphu valley, where he is reported to have lived for about 100 years. He founded the Dechenphug monastery at a location that had been associated since ancient times with Geynyen, a warrior deity.
Later in life, Dampa had an "illegitimate" son named Kuenzang Dorji, who subsequently served as the second abbot of Dechenphug. He, in turn, had a son named Damtrul Loden Gyalpo, who provided evidence at the age of three that he was the reincarnation of his grandfather, Dampa. According to the authors Dorji and Ura, the young abbot could not receive the full teachings of the Drukpa sect given Kuenzang Dorji's advanced age. He instead was sent to Ralung monastery in Tibet to continue his immersion in the esoteric teachings of the Drukpa Kagyu. While there, he came under the tutelage of the 7th abbot of Ralung monastery, Kuenga Sengye (1314-47). After some years of study, they returned together to Dechenphug in 1345, where Kuenga Sengye was "enthroned" (per Sangye Dorji).
Kuenga Sengye was only to live for another two years, but in that short span he established the goenkhang, the fortified tower that still survives today as the heart of Dechenphug Lhakhang. Goenkhangs are usually built to house fierce protective deities—in this instance, the guardian spirit Geynyen, who was the tutelary deity of the Thimphu valley. Kuenga Sangay appointed him as the official protector of the Drukpa Kagyu teachings. Again according to Dorji and Ura, the placement of the tower was such that it "was built lying below the house where Dampa and Damtrul Loden Gyalpo lived and above the drubdeys [retreats for meditation]" (p. 6.) None of these ancillary buildings were built to the same standard as the fortified tower; hence, only traces of their foundations remain.
The co-option of Geynyen into the protector of the Drukpa was not a straightforward matter. Legend asserts that Kuenga Sangay had to subdue the entity and convert the god into a protector deity. According to Tsering, the spirit of Jagpa Melen (another name for Geynyen, meaning "Fire Fetching Brigand and Supreme Warlord" withdrew into a large stone known as the Thimphu, which means "Disappeared into the Stone." It is said that when Bhutan faces its hour of greatest need, the warlord "will come back from the stone and save the country" (Tsering, p. 112). This tale is somewhat similar to the legends associated with the irreverent monk Drukpa Kunley (1455-1529), who subdued a demoness and bottled up her spirit beneath a chorten at the Chime Lhakhang temple. Another similar story is told of the Simtokha Dzong, where the first Zhabdrung Rinpoche (Ngawang Namgyal; 1594-1651) restrained a deity that was terrorizing travelers on the crucial Thimphu-Punakha highway.