The great war between the Helic Republic and the Guylos Empire ended four years ago, but the peacefulness of the world has not returned. In this troubled time, the Republic and the Empire have joined forces and created the Guardian Force in order to stop bandits, rebels, and other troublemakers. Van Flyheight and Fiona join the Guardian Force while continuing their search for Zoid Eve, but unfortunately they have more to worry about than mere bandit and rebels! Mysterious people are involved in a larger and more diabolical scheme, and they even have Organoids of their own!