The Emishi are a summary term for the Jōmon tribes on Honshu. They played an important role in the history of Japan and contribute quite a lot to the modern Japanese culture and society. It is currently a matter of dispute if the Emishi and Ainu are identical or related but culturally distinct Jōmon ethnicities.
The Emishi resisted the Yayoi/Yamato dynasty quite a long time and were feared by the Yamato people. Emishi were known for their war styles and archery skills. The Yamato military was at the beginning no match for the Emishi. The Emishi had a rather easy time defeating the Yamato Japanese until the Yamato adopted the Emishi warfare.
It is suggested that some Emishi joined the Yamato dynasty and were granted high positions. In turn they teached their knowledge to the Yamato.
The famous Japanese bow, the Yumi, is of Jōmon/Emishi origin.
So what happened to them?
After the Yamato conquered the Emishi tribes, they were mostly assimilated into the modern Japanese people. Some tribes resisted quite a long time and retreated deep into the forests to continue a guerrilla war against Yamato Japan. But in the end, they were assimilated. But they left clear traces of their existence and culture.
They and parts of their culture got incorporated into Japanese culture and Shinto. It were also the Emishi descended clans and Emishi influenced clans which greatly refused the introduction of Buddhism and were rather hostile to later Chinese/mainland influences.
Because they had a relatively smaller population than the Yamato agriculturalists, they were rather fast assimilated and outmixed by the Yamato.
Like the Ainu, the Emishi are Jōmon tribes which can be considered as native Japanese. They arrived from Paleolithic Central Asia through Siberia via the Altai mountains to Japan and the Okhotsk sea more than 45,000 years ago.
The Jōmon people were similar to the Cro-Magnon type of people found in paleolithic Europe and Middle East.