Evil parasitic creatures have attacked and infested the tree, and it is up to a band of five intrepid adventurers to take the last seed of their home to safety. Mr. Lantern, Mr. Twig, Mr. Poppy Head, Mr. Feather and Mrs. Mushroom, each with their own abilities are now traversing the strange, botanical environment to deliver the seed and ensure it does not fall in the hands of the parasites.

In Botanicula, players use the different abilities of five strange and amusing characters to escape the dangerous parasites and bring the seed to a safe home.