Crystal Chaser: Tenkuu no Mashoukyuu

For a long time, five magical crystal orbs have been protecting our universe. One of them was hidden on the Earth. But there was a young woman who desired too much power, and she came to the Earth in order to harvest the power of its crystal for her selfish purposes. The only ones who can stop her are Takanoshin, the son of a samurai warrior, and the young girl Noichigo, who teaches little children. Together, they embark on a long and perilous journey through the land of Japan...

[From MobyGames]