Tōji-in, a temple and mausoleum for Ashikaga Takauji (1305–1358) and subsequent Ashikaga shoguns, is a reminder of Kyoto's medieval history as a center of military power. However, in 1863, during the turbulent Bakumatsu period (1853–1867) that marks Japan's transition to modernity, it also witnessed an incident of violent protest. This  incident, the "Beheading of Three Ashikaga Shogun Statues," illustrated the significance of Kyoto and its history for those working to topple the Tokugawa shogunate and, more broadly, demonstrated discontent with the shogunate-style of military governance that had ruled for almost 700 years. Along with other incidents of violent rebellion and terror in Kyoto in the 1860s, these events lent momentum to loyalists who propelled Japan into its first modern civil conflicts. 

Kyoto's transition to a city of the shogunate

As political power shifted from the aristocracy to the samurai military at the end of the Heian Period (794–1185), Kyoto entered a long period as an imperial-military city. 

The Hōgen and Heiji rebellions of the twelfth century destroyed much of the capital and brought it under the control of Taira no Kiyomori (1118–1181), the first of many military leaders who essentially ruled Japan until the modern period. However, under the leadership of Minamoto no Yoritomo (1147-1199), the Minamoto clan defeated Kiyomori and, leaving Kyoto as the imperial capital, set up their capital in Kamakura, beginning the Kamakura period (1185–1333). Yoritomo officially became the first permanent shogun, or "military protector" of the Kyoto-based emperor and wider realm, and established the shogunate system of military rule. 

The Kamakura shogunate ended, however, when their capital was sacked and its military forces destroyed by two generals who defected to Emperor Go-Daigo (1288–1339). In what is known as the "Kemmu restoration," Go-Daigo attempted to establish direct imperial rule. However, one of the generals, Ashikaga Takauji, drove Go-Daigo out of Kyoto, enthroned an emperor from an alternative imperial line, and had himself proclaimed shogun. This initiated a period of conflict between two rival imperial courts (the Northern and Southern Courts period, 1336–1392) and was the beginning of the Ashikaga shogunate (also Muromachi bakufu, 1336–1573). 

The political inroads of military leaders, as well as of militant Buddhist monks and retired emperors, helped shape Kyoto’s prescriptive and imagined borders during this period (Stavros 2014, chap. 4 & 5). Heian-period proscriptions against warriors in the city held, but a new concept dividing the "inside" (rakuchū 洛中) and peripheral "outside" (rakugai 洛外) of the capital emerged, with warriors and their compounds positioned just outside this perimeter. These regulations increasingly blurred from the 14th century. Military generals were granted land in the inner city under the brief rule of Emperor Go-Daigo, and Ashikaga Yoshimitsu, the third Ashikaga shogun, redesigned the city to unify its imperial, religious, and military institutions and place himself at the helm (Stavros 2014, chap. 5). Despite their power, the Ashikaga shoguns mostly abided by norms on constructing military buildings inside the capital, which boosted their legitimacy as rulers.

Tōji-in and the Ashikaga shoguns

Tōji-in (等持院) in Kyoto’s west is said to have been built by the founder of the Ashikaga shogunate, Ashikaga Takauji. Tōji-in is the Ashikaga family temple and mausoleum for Takauji and other Ashikaga shoguns. 

In the early 1860s, a rising tide of dissent emerged against the Tokugawa shogunate, epitomized by the "revere the emperor, expel the barbarians" (sonnō jōi 尊王攘夷) movement. This opposition was rooted in the shogunate's perceived capitulation to western powers through signing the "unequal treaties" and its disregard for Emperor Kōmei's (1831–1867) reservations with the agreements. A significant portion of this opposition was grounded in Confucian ideals in which the shogun's duty was to serve the Emperor within a hierarchical structure aimed at ensuring national harmony. Others followed nativist ideals, such as that developed by Hirata Atsutane (平田篤胤, 1776–1843), which espoused reverence for the emperor, the importance of preserving the "purity" of the sacred imperial soil, and a return to ancient ways (Walthall 1995). 

In 1863, nine of Hirata's disciples beheaded statues of the first three Ashikaga shogun and displayed the heads on the banks of the Kamo River south of the Sanjo Bridge (Walthall 1995, also Keene 2006). All declared themselves loyalists (shishi 志士) and hailed from multiple backgrounds, including ronin (masterless samurai), shrine priest, merchant and peasant. Their act mimicked assassins loyal to the emperor, mostly ronin or samurai, who over previous months had killed supporters of the shogunate and displayed their heads nearby on the river or in other prominent locations in the city (Walthall 1995). They targeted the Ashikaga as they saw them as traitors of the emperor: Takauji for overthrowing Emperor Go-Daigo, and Yoshimitsu (1358–1408, the third Ashikaga shogun) for declaring himself king and submitting to China. Their decapitation of the statues was also a criticism of shogunate authority generally and an ultimatum to the Tokugawa shogunate to submit to and serve the Emperor, specifically by repealing the treaties with western powers. 

Unlike the assassins, who had been treated with tolerance, group members were violently rounded up and threatened with execution. Petitions of support saved most of their lives, though they were still exiled from Kyoto. As Anne Walthall argued, at a time in which samurai dominated the political sphere, including as assassins terrorizing Kyoto, and social hierarchy was strictly enforced, this "political prank" demonstrated the potential of people from a diversity of social backgrounds to act politically in support of the emperor (1995, p. 170). The incident, and support for its perpetrators, therefore reflected broader a shift toward recognizing the ability and agency of men irrespective of their social rank. 

More than just a prank, however, this incident was one of many that built opposition to the Tokugawa, which sparked conflict in the capital and culminated in the Battle of Toba-Fushimi in the south of Kyoto (January 1868), the beginning of the Boshin War (1868–1869). As illustrations of the scene (see below right) from early 20th century publications about the Edo period highlight, this incident maintained significance for modern readers even half a century later, perhaps due to its alignment with modern values regarding the political empowerment of commoners.