The Boy Who Saw the Wind(2000)

Kaze wo Mita Shounen

Young boy Amon has mysterious powers. His dad is the cheif scientist for the Empire of the Golden Snake. He's invented weapons for this country in the past, but does not want his boy's powers to be used for destruction so he burns his research and tries to escape the country with his family. The mom and dad die in the escape and only Amon is left. He runs from the military, ends up on an island where he learns about the ancient people who could fly on the wind and talk to animals (as he can). Amon then ends up in a fishermen's village and makes friends with Maria. After this village is attacked by the Golden Snake army, the two run away with a band of rebels. Together, they try to stop the Empire of the Golden Snake from destroying and conquering everything. Based on the book by C.W. Nicol.