Super Mario Bros. Wonder is a side-scrolling platform game. As one of twelve player characters—Mario, Luigi, Princess Peach, Princess Daisy, yellow and blue Toads, Toadette, Nabbit and four types of Yoshis—the player completes levels across the Flower Kingdom with assistance from its flower-like denizens. Similarly to previous Super Mario games, players guide their character to the end of a level while avoiding enemies, such as Goombas and Piranha Plants, and transporting through Warp Pipes. Each stage contains multiple collectible "Wonder Seeds".

New power-ups include a fruit that transforms the player into an elephant, a flower that allows the player to create bubbles that capture enemies, and a mushroom that gives the player a drill hat that allows them to burrow into the ground or ceiling to evade enemies or bypass obstacles.

Wonder introduces the Wonder Flower, which triggers bizarre effects such as pipes coming to life, hordes of enemies spawning, and character appearances and abilities changing. The effects end when a player collects a Wonder Seed or leaves the area of effect.

A new feature allows players to equip badges, which are unlocked throughout the game and give different advantages to the player. They are divided into three different categories: Action Badges, which grant the player character an additional ability; Boost Badges, which give the player character an additional passive ability; and Expert Badges, which grant the player character an advanced skill. Only one badge can be activated at a time per level. They are usually optional and can be shut off for higher difficulty.

The game supports local multiplayer for up to twelve players in a room with a limit of four players active in a level. It also has some online multiplayer functionality. When playing through a level while playing online, translucent versions of up to three other players playing through the same level may be present. When other online players are present nearby, defeated players become ghosts and are given a short window of time to revive themselves by flying toward another player or a standee placed by another player.

Mario and his friends are invited to the neighboring Flower Kingdom by its ruler, Prince Florian, to see a demonstration of a Wonder Flower; great treasures of the Flower Kingdom that can warp reality. Bowser interrupts the ceremony and seizes the Wonder Flower, using its power to merge with Prince Florian's castle, turning himself into a giant flying fortress and imprisoning the citizens of the Flower Kingdom. Mario and his friends volunteer to help Prince Florian stop Bowser, prompting the prince to accompany the party. As the gang work to save the captured Poplins, they realize that by gathering six Royal Seeds, which are considered precious treasures in the Flower Kingdom, they will grant access to Castle Bowser, as each time a Royal Seed is collected, it destroys one of the six Cloud Piranhas protecting Castle Bowser.

After freeing the various regions of the Flower Kingdom from the control of Bowser Jr. and removing Bowser's defenses, Mario and friends confront Bowser on his flying castle, where he reveals his plan to use the Wonder Flowers' power to enslave the universe with rhythm. The party defeats Bowser and returns the Flower Kingdom to normal, while Bowser, Bowser Jr. and Kamek flee.

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