The Japanese emerged from a relatively closely-related group of bronze age settlers sharing a similar culture/religion that migrated to the Japanese archipelago from the Korean peninsula, give or take 3000 years ago. Around 2500 years ago, a dominant tribe/clan (the Yamato) established military/political hegemony over this group. This was also the origin of the first and only royal dynastic house in Japan. At the same time, they were also conquering and assimilating the weaker hunter-gatherer tribes that had settled the islands earlier.

The emperors of this royal house claimed they are direct descendants of the sun goddess (Amaterasu), hence have a divine sanctioned authority/right to rule the other Japanese tribes and clans. And from this basis, the Japanese were able to establish and sustain a socially/culturally homogeneous society for the last two thousand years.

The Yamato emperors ruled pretty much uncontested up until the 1100s, and even when the country splintered into territories de-facto controlled by military strongmen, the emperor still held a paramount religious and spiritual role for the country (like the Pope for Catholics).