In a hospital in Tokyo, a university professor named Kenji Murai is visited by a man who asks him about the events that led him to the hospital. The story is about a group of crew and passengers on a day trip on a yacht, including Murai; his shipmate assistant Senzô Koyama; writer Etsurô Yoshida; celebrity Masafumi Kasai, the owner of the yacht and two female passengers, professional singer Mami Sekiguchi and student Akiko Sōma. A sudden storm causes the yacht to nearly capsize, causing it to drift uncontrollably. The group arrive at a seemingly deserted island and begin to explore. They come across ponds full of fresh rain water and a large forest of mushrooms. The yacht's skipper, Naoyuki, warns them not to eat the mushrooms because they might be poisonous.

As they cross the island, they come upon a shipwreck on the shore whose sails are rotted and its interior is covered with a mysterious mold. Finding that the mold succumbs to strong cleansing products, they work to clear it from the ship. In doing so, they begin to suspect that the ship has been involved in some sort of nuclear testing of the polluted waters, forcing a bizarre mutation on various organisms, including the mushrooms. As the days pass, the group grows restless as their supply of food stores starts to run low. Masafumi Kasai refuses to help find a way off the island and steals from their food stores instead. After becoming concerned about their provisions, Yoshida decides to try eating the mushrooms.

One night, as Kasai is raiding the food stores, he is attacked by a grotesque-looking man who promptly disappears after encountering the group. Suddenly, Yoshida's behaviour begins to grow erratic, leading him to be locked inside Kasai's room right after he pulls a gun on the group. Naoyuki decides that in order to survive, the team must leave the island. The others disagree, leading him to depart on his own. Mami frees Yoshida and they attempt to take over the ship, shooting and killing Senzô in the process. Kenji and Akiko manage to take control from the two and force them off the ship. Kenji finds the yacht adrift and swims out towards it. He finds Naoyuki missing and a note left behind explaining that he is responsible for the deaths of his group and had jumped overboard. On the ship, Kasai is confronted by Mami, who entices him to follow her into the forest. Perpetual rainfall has caused wild fungal growth, and Kasai realizes that those who have been eating the mushrooms have turned into humanoid mushroom creatures themselves. The mushrooms are addictive and cannot be resisted after the first bite. Kasai is last seen collapsing as mushroom creatures begin to swarm him.

Others who have turned into mushroom creatures attack Akiko and Kenji. They are separated and Akiko is kidnapped. As Kenji tracks her down, he discovers that she has been fed mushrooms and is under their influence along with Mami, Yoshida and Kasai. Kenji attempts to rescue Akiko, but he is overwhelmed by the mushroom creatures and flees without her, making his way onto the yacht and escaping the island. Several days pass before Kenji is finally rescued. As he waits in the hospital, he begins to wonder if he should have stayed with Akiko on the island. His face is revealed to show signs of being infected with fungal growths. Kenji states after that it did not matter whether he stayed or not, but he would have been happier there with Akiko. The screen fades as Kenji notes that humans are not much different than the mushroom creatures.