After Nisshin, the various Nichiren Buddhist lineages within Kyoto struggled with each other. Each faction claimed that it alone truly upheld Nichiren Shonin's teachings. Many of these factions took up the practice of fuju fuse and vigorous shakubuku. In 1451, for instance, Myomanji Temple created a set of regulations even stricter than those set forth by Nichijo of Myokakuji Temple back in 1413. Eventually, the various Nichiren Buddhist temples realized that they would need to set aside their conflicts in order to present a united front against the forces of the warrior monks of Mt. Hiei which threatened them. This resulted in the Kansho Accord of 1466. The Kansho Accord contained six principles on which all the temples of Kyoto agreed, with the exception of Honpoji Temple of Nisshin's lineage. The six principles were:
1. The identity of the theoretical and essential sections of the Lotus Sutra, though one or the other may be considered superior depending on people's capacities and level of understanding. This principle attempted to reconcile the shoretsu (superiority of the essential section) and itchi (harmony of both sections) doctrines.
2. All Nichiren Buddhists, both monastic and lay, should practice shakubuku.
3. Nichiren Buddhists are prohibited from making pilgrimages to the temples or shrines of slanderers.
4. Nichiren Buddhists are not to receive offerings from slanderers, unless those offerings are made for secular reasons.
5. Though shakubuku (the way of subduing slander) and shoju (the way of embracing what is true) are both ways to teach the Dharma, shakubuku is now the proper one to use. This is a reiteration of point two.
6. Lay followers should not forsake their original teachers, though they may give offerings to more than one temple if those temples all agree to it.
The Kansho Accord did not last for very long. The Onin War of 1467-1477 was particularly destructive, and in 1469 the Tendai warrior-monks burned down much of the aristocratic northern part of Kyoto. The Nichiren temples were in the southern part of the city, so they became rallying points for the merchants who lived there. The townspeople (machishu) formed their own militias to protect themselves from the warrior-monks of Mt. Hiei, peasant rebellions, and warlords from the provinces. Since many of them were Nichiren Buddhists, the temples became virtual fortresses. At this point, the temples resumed their struggle for power.
Nisshin (1444-1528) was a monk who studied at Myohonji Temple (the former Myokenji Temple). He was an adherent of shoretsu, and in particular he emphasized the superiority of the 16th chapter. Eventually he left Myohonji and founded Honryuji Temple in Kyoto in 1489. The Honryuji Temple is now the head temple of the Hokke Shu Shin-Monryu (founded 1488). With the creation of a new sect by Nisshin, the Kansho Accord was shown to be totally ineffective in ending sectarianism.
Despite the power struggles and doctrinal conflicts, the Kyoto temple militias gained in strength as the Ashikaga Shogunate's power waned and Japan descended into anarchy. When the Nembutsu based peasant rebellions threatened the city of Kyoto in the summer of 1532, the militias came out in force to defend the city, and for the next four years they ruled the city of Kyoto. This brief rule of the Nichiren Buddhist townspeople is known as the Lotus Uprising (Hokke Ikki) in contrast to the Pure Land Buddhist peasant rebellions known as the Single-minded [Faith in Nembutsu] Uprisings (Ikko Ikki).
The Lotus Uprising ended disastrously in 1536 when a Nichiren Buddhist lay follower challenged and then defeated a Tendai monk in a public debate. Incensed, the warrior-monks of Mt. Hiei descended upon the city in force and burned down all 21 of the Nichiren Buddhist head temples in Kyoto as well as the whole southern half of the city and a good portion of the northern half. This event is known as the Tenmon Persecution.
After the Tenmon Persecution, many of the Nichiren Buddhist clergy and lay followers took refuge in Sakai near Osaka. In 1542 they were finally allowed to return to Kyoto. By 1545, 15 head temples had been reestablished. Once again, the temples were forced to put an end to sectarianism in order to present a unified front against Mt. Hiei and their other enemies. In 1564 the 15 temples signed the Eiroku Accord in which they attempted to reconcile the shoretsu and itchi factions of Nichiren Buddhism. This agreement was extended by the Tensho Accord of 1575. In spite of their new found unity, and the razing of Mt. Hiei by the dictator Oda Nobunaga in 1571, the Nichiren Buddhist temples of Kyoto would never regain the power and prestige they had attained at the height of the Lotus Uprising.
Oda Nobunaga's destruction of Mt. Hiei was not done as a favor to the Nichiren Buddhists of Kyoto. In fact, Nobunaga was determined to bring all of the Buddhist schools under his firm control. In 1579, he decided to teach the Nichiren Buddhists a lesson they would not soon forget. In that year he demanded that a debate be held in Azuchi Castle between representatives of Nichiren Buddhism and Pure Land Buddhism. Despite the superior arguments of the Nichiren Buddhist monks, Nobunaga declared the Pure Land monks the winners and condemned the three main Nichiren Buddhist representatives to death. He then demanded that the Nichiren Buddhists pay reparations to the Pure Land school, sign an admission of defeat, and cease all proselytizing in Kyoto. This is known as the Azuchi Persecution. After the Azuchi Debate, the major schools of Nichiren Buddhism emphasized the shoju method of propagation rather than the shakubuku method.