Situado no ano de 2000 (entre os eventos de Patlabor e Patlabor 2), quando o nível de acidentes de trabalho começa a aumentar em torno da Baía de Tóquio, os detetives da polícia Kusumi e Hata são designados para investigar. O que eles descobrem leva a uma série de encobrimentos do governo, conspiração relativa a uma nova arma biológica intitulada Treze Desperdiçados WXIII e uma conexão pessoal trágica com Hata. A única esperança de acabar com essa ameaça é cooperar com os militares e levar o WXIII a um confronto com o Labors of Special Vehicle Division 2.
The film begins with some Polaroids of a young boy and a young girl. A female voice over tells us who these people are...they are brother and sister, she is seven and he is eight. She goes on to say that when she was seven and he was eight, she told her brother that she would marry him.
In a land filled with magic and mystery, two rival kingdoms are readying for war: Isa, the beautiful water-laden city, and Paro, the industrialized wasteland. Windaria follows the tale of two sets of lovers: Marin and Izu, a young pair of farmers who are devoted to one another, and Ahanas and Jill, princess and prince of the rival kingdoms. With war approaching, these star-crossed lovers will experience the true depth of tragedy as they struggle to survive.
