Dry Bowser meets with Wart,whom he makes an agreement to have power for the staff as an exchange to make him whole again. Dry Bowser was aware that Mario and Peach are going vacation so he has two secret weapons to do the job.
Mario,Peach,and Toad arrived at Isle Delfino when they notice a paint like goop.
They notice a Parachute holding a box has landed. As the box opens,out of it is the Flash Liquidizing Ultra Dousing Device,also called F.L.U.D.D.,a water cannon created by Professor . After cleaning the goop,Mario is arrested on suspicion of vandalizing the island with graffiti,which caused the source of the island's power,Shine Sprites,to disappear and the island to be covered in shadow.
While Mario begun cleaning up the mess around the island,The Culprit appeared,revealing to be a Shadowy Blue doppelgänger of Mario known as Shadow Mario,who was using a Magic Paintbrush to create the graffiti. Shadow Mario kidnapped Princess Peach and Mario is confronted by Petey Piranha.
After defeating the monster,Mario confronts Shadow Mario and destroys the Paintbrush,causing Shadow Mario to morph into Bowser Jr.,a Koopa made from Bowser's DNA. Dry Bowser appears and reveals that He stole the Paintbrush that was created by so that Jr can use it to frame him. He gave Wart the Shine Sprite so that he could power the staff.
Unfortunately,Wart uses the staff to create the Storm to blow away half the town. Mario begun trying to stop Wart,who tried to blast him,but hits Dry Bowser instead. Mario manage to destroy the staff,releasing the Shine Sprites and storm clouds disappears. Mario has freed Peach and tries to escape with F.L.U.D.D.,but Wart grabbed his foot. Suddenly,Dry Bowser appears,now fully whole, and incinerates Wart with Blue Flame.
The people of Delfino congratulates Mario before He relaxes in the Sun with Peach.