Alchemy is a pseudo-science that attempts to create gold from various different combinations. One experiment to do so artificially brings to life a race of creatures known as the Chemies, made to imitate things that exist in the world, such as grasshoppers. Stored in Ride Chemy Cards, they were accidentally released all at once.

Houtarou Ichinose is entrusted with the Gotchardriver and the mission to recollect the Chemies. Some are friendly, and Houtarou can fuse with them to transform into Kamen Rider Gotchard. However, if influenced by human malice, they may birth monsters known as the Malgam. This is a story that explores the nature of good and evil, which are two sides of the same coin.