Nausicaä is the Princess of the Valley of the Wind, a small nation on the outskirts of the Empire, and near the Sea of Corruption. She possesses the unique ability to communicate with the Ohmu, the giant insects that protect the fungal forest. While returning from the Sea, she finds enraged Ohmu, and stops them, but not before they can destroy the ship they were chasing. A young woman gives Nausicaä a stone with her dying breath and says she must return it to her brother in Pejite City.

Back in the Valley of the Wind, Nausicaä meets with her dying father. She decides to take up the role as gunner for the Valley in the Torumekian army. Meanwhiile, Princess Kushana discover the stone (which can activate a Giant Soldier) is in the Valley of the Wind. She races there to obtain it, but Nausicaä refuses to let them in for fear of infecting the Valley with spores from the Sea of Corruption. War breaks out, and they must all leave, Nausicaä joining the Torumekian in her gunship.

Nausicaä's ship is shot down by the remnants of Pejite city, and she is forced to crash land in the forest. She rescues Asuberu from an Ohmu attack, and then learns he is the brother who she was searching for. She hands over the stone. They find themselves in a place under the forest which has been cleansed from the sickness. They are then captured by Doruku. Nausicaä escapes, with the blessing of a priest, and returns to Kushana.

After a battle in which Nausicaä is able to release Doruku prisoners she heads off to see where the Ohmu are heading in a herd. She finds an old monk in a shrine who tells her that a new world would be created through purification. She follows a swarm of insects that are chasing a Doruku battleship spewing poisonous gas in the region.

The ship, it turns out, was spreading the growth of new corrupted forest through the use of a man-made fungus. The fungus, however, was out of control and consuming the ship. They attempted to destroy the fungus, but were not entirely successful, and Nausicaä only barely escaped the ship alive.