Wind's Seed tells the story of sister and brother, Meena and Otto, who possess the unique power of "call", allowing them to focus spiritual energy in order to cast magical spells. Once they arrive in a small village, they are asked to go to the Western forest, presumably to help gather some healing plants. However, they soon learn that it was a trap, and must defend themselves in order to survive...

Even though it looks like a side-scrolling action game, Wind's Seed is essentially a "light" Japanese-style RPG, with the characteristic random enemies, turn-based combat, and automatic leveling up. There are also peaceful areas with inns and shops, where they can acquire healing and support items. The player controls only Meena and Otto. In every battle, it is necessary to raise the "call level" of them, in order to unleash more damaging spells; with a low call level, they won't be able to defeat their foes. Otto also has the ability to heal the party.