Before you begin looking into the history of Japanese 'warrior monks', it's important to look at the translation of the term sohei - so as either priest or monk, and hei as soldier or warrior - thus, sohei were literally priest warriors. In Stephen Turnbull's book Japanese Warrior Monks, Turnbull makes a comparison between Japanese sohei and the Teutonic Knights, whereby the warriors were not all necessarily ordained, or officially made a minister. These warriors are similar to many Japanese sohei, in that the organisations of warrior monks would be under religious control, and served as the military arm of various temples.

Another bit of background - whilst the imperial court had no official control over the various temples, the emperor had the right to appoint the head abbot of the temple - this point was the spark that kickstarted the first temple feuds.

Unlike the religious wars often seen in other parts of Asia and Europe, the first conflict seen between various temples did not involve doctrine or dogma, but rather simple politics. Throughout the mid-late 10th century, various arguments came up between temples against temples and temples against the imperial court, several times escalating into fights and brawls that led to monks being killed. The famous temples during this period were the Enryakuji, Todaiji, Miidera, and Kofukuji.

During the late Heian period in the 12th century, Japan became embroiled in a conflict known as the Gempei War, fought between the Taira and Minamoto clans, with both sides attempting to curry favour from the religious armies. In 1180, the Minamoto, through a Prince Mochihito, raised a rebellion against the ruling Taira clan in Kyoto. They swiftly crushed the rebellion, and Mochihito fled to Miidera, whereby both the rebel army and the warrior monks fled further south in hopes to gain reinforcements from the Nara temples - Miidera was razed to the ground. The Battle of Uji saw a famous stand by the monks and samurai of the rebellion, and was the first reckoning of their power, soon followed by the massacre by the monks of sixty samurai sent by the Taira. In retaliation, the Taira besieged Nara and burnt it, as well, to the ground.

Enryakuji was the last standing monastery, and so this essentially marked the end of sohei dabbling in the politics and conflicts throughout the rest of the Genpei War. Sohei appeared again throughout the Kamakura and Muromachi period, and notably as well in the Sengoku period, with the Ikko Ikki being a famous example of a powerful monastic contingent, though I guess that sort of falls out of the bounds of your question.