Wario's Woods is a puzzle game similar to Tetris or Columns, but with a twist. Instead of directly controlling the monsters and bombs that are falling down, the player controls Toad who has to carry around stacks of monsters and bombs and to combine them in the right way. One bomb plus at least two monsters of the same color have to be combined to make them disappear. If five or more objects are cleared at the same time, a diamond will appear. Destroying the diamond will clear all monsters of the diamond's color.

The Peaceful Woods was once the friendly home of sprites and other gentle forest creatures. Wario and his band of monsters invaded, though, and spoiled the serenity of the woods. The quiet, woodlands community has now been turned upside-down by these horrifying events. Wario has now named the woods after himself, and peaceful creatures are not welcome. Toad, the Mushroom Kingdom hero, has decided to travel to Wario's Woods and put an end to Wario's evil reign of terror. Toad knows that, with the sprites help, he will be able to rid the forest of Mario's twisted nemesis. Thankfully, the sprites are able to create bombs. It's Toad's job to line up the bombs with the enemies of the woods, thus defeating those evil creatures. By clearing more and more of the woods, Toad steps ever close to the ultimate challenge of facing Wario.