Two pairs of young lovers are drawn into a conflict between two opposing kingdoms: the primitive yet splendid Isa and the militaristic yet unruly Paro. Izu and his wife Marin work as simple farmers in the humble village of Saki, situated directly between Isa and Paro. Though Saki lacks the elegance of Isa or the war engines of Paro, the village is home to a magnificent tree called "Windaria," to which the villagers offer their prayers in exchange for "good memories."
When war breaks out, Izu decides to enlist in Paro's army, lured by the promise of a fantastic motorbike given to him as a bribe. Before he leaves, the couple makes a mutual promise: he will definitely return to her, and she will wait for him until he does. The other pair consists of Jill, the prince of Paro, and Ahanas, the princess of Isa. Initially they want no part in the rapidly escalating war, but after Jill's father—the king of Paro—dies by his son's hand during an argument over the conflict, Jill has little choice but to carry out his father's final wish: the conquest of Isa.
The only complication is that Jill had sworn to his beloved Ahanas that he would not get involved. Windaria is a war parable set in a fantasy land filled with unicorns and ghost ships.