An ichorous green meteor plummets through the Earth's atmosphere, fracturing and showering the earth with glowing green space dust that affects all forms of life nearby. Some plant life - mushrooms and cacti - acquire sentience while, the meteor twists and mutates other life forms, transforming insects and animals into semi-intelligent, warlike communities.

Mushroom Men – Rise of the Fungi throws gamers into the action at the point when the different Mushroom nations form, with each claiming a different part of the world as their exclusive territory. The Bolete Tribe and the Morels live in isolation and thrive for a time in peace and quiet. The Amanitas Empire considers themselves superior to the Bolete and the Morels and remains segregated from the other nations until they build forces strong enough to conquer everyone. The Mushroom Men face many threats in this hostile new world. Their size makes them targets for all manner of creatures: spiders, beetles, hornets, and other creatures that threaten to destroy their villages. The Amanitas therefore build their forces by consuming the prosperity of other groups. Raging territorial attacks lead to the terrible Spore Wars. The mysteries of the Mushrooms' origins fade completely into myth, a riddle that promises great knowledge and power to the one who can find its answer...

Mushroom Men – Rise of the Fungi tells the story of the birth of the Mushroom Men. It starts out with the simple tribe of Bolete learning to live off the land. They struggle against their environment for a time until the Amanitas Empire arrives. To their dismay, the Bolete learn that their fellow Mushroom Men aren't any better than the hostile insects and other creatures that threaten them.