The assault began with Sakamoto.

Sakamoto was the town at the base of Mount Hiei, home to the temple attendants, craftsmen, merchants, and families who had built their lives in the long shadow of Enryakuji. During the night, seeing the troop movements below, many of its residents had fled upward toward the temple complex — toward what 600 years of precedent told them was the safest place they could go. By the morning of September 29, 1571, Nobunaga's three-column force had already sealed the mountain completely. Sakamoto's residents had run directly into the enclosure.

Nobunaga established his field headquarters at the mansion of Yamaoka Keigaku as his forces swept through Sakamoto and began their ascent. The operation divided into three simultaneous lines of advance: one from the west, one from the south, one from the eastern slope above the lake. The 僧兵 (sōhei) — the warrior monks who had maintained Enryakuji's reputation as a military force since the 10th century — fought at multiple points on the slope. They were outnumbered at every position and cut down piecemeal.

The fires on the mountain were visible from Kyoto.

The killing was not limited to armed resistance. Nobunaga's men moved through the temple buildings hunting survivors. Those who fled downslope were already encircled. According to contemporary accounts, monks who reached the lower paths were thrown back into the flames. The residents of Sakamoto who had sought refuge at the summit died alongside the priests. The 焼討ち (yakiuchi) — the term Japanese historical literature uses for this event specifically — was a burning raid in the most complete sense: it did not distinguish between soldiers and civilians, between monks who had raised weapons and those who never had.

The assault on September 29 continued through September 30, when Nobunaga ordered a full total assault from all commanders. By the time it was over, somewhere between 1,500 and 4,000 people were dead. Approximately 300 buildings had burned to the ground. Archaeological work by Yasuaki Kaneyasu has found that only the Nemoto Nakado and the Grand Lecture Hall can be definitively confirmed as destroyed in Nobunaga's attack — many structures had been damaged or eliminated in earlier centuries of inter-temple rivalry. Of the vast complex, one hall — the 瑠璃堂 (Ruridō) — was said to have survived. Why that single building endured, the sources do not say.

The Jesuit missionary Luís Fróis was somewhere below the mountain during this period. In his chronicles, he recorded what was left when the fires had gone out: nothing moved on the mountain save badgers and foxes crossing a carpet of ash. Fróis was appalled by the scale of the killing, and yet — because he saw Buddhist institutional power as an obstacle to Christian conversion in Japan — he had found in Nobunaga something useful. He wrote of hoping that Nobunaga might eventually be persuaded of Christianity's truth, and in the meantime was content to find an ally against the Buddhist hierarchies that had blocked Jesuit work for decades. It is one of the more unsettling observations in the historical record of this period: a European priest, watching a mountain burn, finding the silver lining.

For the 僧兵 (sōhei) as an institution, September 29, 1571 was the end. The warrior monk tradition had operated as a force in Japanese politics since 970 CE, had shaped the Heian court, had made and broken alliances across the Kamakura and Muromachi periods. It ended in a morning. No religious institution raised an army against Nobunaga again. The daimyo who watched from their castles across central Japan — men who had always calculated whether any alliance with the temple might be useful — understood immediately that this calculation no longer applied.

Emperor Go-Shirakawa's famous lament — that three things refused his will, the Kamo River floods, the fall of dice, and the monks of Enryakuji — had been half-joke, half-despair: the resignation of a ruler confronting something too embedded in the world to move. After September 29, it was an epitaph.

The temple was eventually rebuilt, but never recovered its political power. The Tokugawa era that followed Nobunaga's campaigns was an era without armed monks. Enryakuji today stands as a UNESCO World Heritage Site — rebuilt, restored, and entirely peaceful. The mountain that Nobunaga burned is now one of the most serene places in Japan. History contains these ironies and moves on.