The vendetta between the Minamoto and Taira clans erupted into the conflict called the Gempei Wars. It was a series of battles fought for the control of the imperial court and the ultimate victors were the Minamoto who annihilated the Taira and established their clan head, Yoritomo, as shogun and consigning the emperor to nothing more than a symbolic role until the mid-19th century.

The invasions of Khubilai Khan's formidable Mongol army is one of the most memorable events of Japanese history. Twice Japan was saved from almost certain doom by the formidable forces of nature in the legendary divine wind.

In 1318 a new emperor called Go-Daigo came to throne and attempted to restore the power of the imperial court over the shogunate. The result were the Nanbokucho Wars or the Wars between the Southern and Northern Courts. In the end the Northern Emperors were victorious whose line continues in the Japanese imperial family of today.

A precursor to the Sengoku Jidai, the Onin War began as a quarrel between two rival families who used succession over the shogunate as an excuse to destroy each other. The conflict escalated until it enveloped Kyoto itself, almost destroying it. The Ashikaga shoguns became mere puppets after the Onin War but something more serious had happened as Japan fragmented into independent states heralding the beginning of the Sengoku Jidai.