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Most references indicate that Amaterasu decided that Japan needed an emperor and she sent her grandson, Ninigi, to rule; however, they always refer to his grandson (great-grandson), Jimmu, as the first emperor.

edited: Further research shows that he ruled in an area near Kagoshima and Jimmu established rule in Yamato. Is it merely a matter of Ninigi's location not being the "heart" of Japan that prevents him being called the first emperor?

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    Note that Amaterasu sent Ninigi to rule 'Ashihara no Nakatsukuni', which is not fully synonymous with Japan. Whereas after Jimmu launched his conquest of the east, he becomes described as "ruling the world (i.e. Japan)" / "acceded to the imperial title". So a tautological answer here is because Ninigi wasn't an emperor of Japan. Of course, that's not very helpful.
    – Semaphore
    Dec 16, 2021 at 9:14

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Ninigi No Mikoto in Japanese mythology is said to be the divine origin of the Yamato clan. There are several versions of the myth, in both the Kojiki and Nihon Shoki. In the latter there also are several versions.

In one version, he is given the task of ruler of Earth after his father Ame-No-Oshihomimi-No-Mikoto refuses.

In another version, Amaterasu-Ōmikami sends Ninigi to replace the failed rule of Ōkuninushi.

Whatever the version, the crux is that Amaterasu gives the job to Ninigi. Ninigi came down from heaven to Mount Takachiho in the land of Himuka and built his palace there. Several of the oldest clan families are mentioned as serving the Yamato (the name of the imperial family) at this point, like the Nakatomi and the Inbe.

However, at this point, there are still many rivaling clans throughout Japan. This is why Ninigi is not regarded as the first emperor.

His grandson's conquest of Japan and the establishment of the imperial court is told in the myth of the Yatagarasu. This great crow was sent from heaven as a guide for legendary Emperor Jimmu on his initial journey from the region which would become Kumano to what would become Yamato, (Yoshino and then Kashihara).

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    To add to this, Ninigi and the next two generations are said to have ruled Kyushu; Jimmu's conquest took him to Yamato, which is now central Japan.
    – Semaphore
    Dec 16, 2021 at 8:35

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