Originally Posted by A Wikipedia article kindly

Each year for the past ten years, purple clouds have mysteriously appeared in the sky, signalling misfortune and disaster for people across the world.

After years of torment at the hands of a "land shark" which ravages their village each time the clouds appear, youths Shu, Kluke, and Jiro hatch a plan to fight back against the monstrous fiend. However, in the course of attempting to stop it, they discover it is not a creature at all, but rather a strange machine. After scuffling with the trio, it leaves the village and eventually takes flight, returning to a mother ship high in the purple clouds, taking the three heroes with it.

At the mother ship, they are subjected to constant attacks from metal soldiers. Exploring further, they encounter the ship's captain, an ancient man named Nene. Revealing that he has been behind the yearly attacks on the village, Nene apparently delights in the anguish he causes. Shu and the others are outraged and attempt to defeat him in combat, but he easily defeats them. After barely escaping to a nearby hangar, the three discover a smaller ship docked within, but lack the necessary skills to pilot it. At this point, three small spheres of light appear, and a disembodied female voice instructs them to swallow the spheres in order to gain both power and the ability to pilot the craft. The three youngsters do so, and immediately find that their shadows have grown into monsters; Kluke's becomes a blue phoenix, Jiro's a blue minotaur, and Shu's a blue dragon. They then hastily make their escape aboard the smaller ship, exercising sufficient flying ability to get them down to the ground before it crashes.

Following their escape from Nene's air fortress, the heroes (and several others who join with them) gradually traverse and explore the continent. In the process of doing so, they encounter other people from others towns that have also fallen victim to the purple clouds in one form or another. Struck by the injustice and harm that has been inflicted, they decide that they must stop Nene from continuing to bring ruin upon their world.