From the Super Mario Wiki
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Bowser, at his summer villa on Vibe Island, discovers its power and ability to control characters' emotions. Bowser successfully uses Army Hammer Bro and Hammer Bros to find and retreive the wand. The Koopa Troop also successfully uses a Goomba to kidnap Mario, Luigi, and several Toads. This Goomba, affected by the Joy vibe, however, misuses the Scepter, and creates the same havoc in Bowser's Villa and Vibe Island as seen in Peach's Castle.
When Toadsworth, Peach, and a Toad discover what has happened, Princess Peach decides to rescue the Mario Bros., taking Perry with her. Peach encounters several enemies affected by the Vibe Scepter on her adventure, but doesn't know this until the final fight with Bowser.
During the first part of her battle with Bowser, he takes advantage of several different Vibes. In the second half, Bowser uses the power of the scepter to increase in size and strength. However, Peach defeats Bowser and knocks him over the horizon, making him drop the Vibe Scepter. Later, the ending sequence suggests that it is somehow found in the player's own home.