The game takes place on Isle Delfino, a dolphin-shaped tropical island mainly inhabited by the Pianta and Noki people.
Mario sets out for Isle Delfino for a vacation with Princess Peach, her steward Toadsworth, and several other Toads. Upon arrival at Delfino Airstrip, they discover a mass of paint-like goop. After acquiring the Flash Liquidizing Ultra Dousing Device (F.L.U.D.D.), a water cannon created by Professor E. Gadd, Mario defeats a slime-covered Piranha Plant that emerges from the goop. However, Mario is arrested on suspicion of vandalizing the island with graffiti, which has caused the source of the island's power, Shine Sprites, to disappear and the island to be covered in shadow. After being convicted, Mario is assigned to community service in order to clean up the island and track down the real criminal.
The culprit is revealed to be a shadowy blue doppelgänger of Mario known as Shadow Mario. Using a magic paintbrush, also developed by Professor E. Gadd, Shadow Mario created the graffiti. He attempts to kidnap Princess Peach, but is thwarted by Mario. After the player collects 10 Shine Sprites, Shadow Mario successfully kidnaps Peach and takes her to Pinna Island. Upon arriving at Pinna Park, a theme park on the island, Mario encounters and destroys Mecha Bowser, a giant Bowser robot controlled by Shadow Mario. Afterwards, Shadow Mario reveals that his true identity is Bowser Jr., Bowser's son, and that he framed Mario because his father, Bowser, told him Peach is his mother, whom Mario was trying to kidnap. Mecha Bowser's head then transforms into a hot air balloon and Bowser Jr. takes Peach to Corona Mountain.
After the player defeats Bowser Jr. in his Shadow Mario disguise in the 7 main levels, Delfino Plaza floods and the entrance to Corona Mountain is opened. Mario travels through the lava-filled caverns and finds Bowser, Bowser Jr. and Princess Peach in a giant hot tub in the sky. Mario defeats Bowser and Bowser Jr. by destroying the hot tub, causing everyone to fall from the sky. Bowser and Bowser Jr. land on a platform in the ocean, while Mario and Peach land on a small island. However, F.L.U.D.D. is damaged by the fall and powers down. Mario and Peach watch as the Shine Gate's power is restored while a group of Piantas and Nokis celebrate. Meanwhile, Bowser admits to his son that Peach is not his mother, to which Bowser Jr. replies that he already knows, and that when he is older he wants to fight Mario again. Mario and Princess Peach watch the sunset at Sirena Beach, and the Toads present Mario with F.L.U.D.D., who has been repaired, and he declares the vacation begins now.
F.A.Q.
How to Obtain Sunglasses & Shirt: To obtain the sunglasses, the player must collect 30 Shine Sprites and talk to the pianta in Deflino Plaza who will outfit Mario with sunglasses. The sunglasses have no apparent function besides slightly darkening the screen, thereby reducing the bright effects of the sunlight. To obtain the shirt, the player must defeat Bowser at Corona Mountain and talk to the same pianta who will outfit Mario with a sky-blue shirt with small Shine Sprite images printed on it.
Reward for 120 Shine Sprites: After collecting all 120 of the Shine Sprites and defeating Bowser in Corona Mountain, the ending graphic is replaced with a group picture of friendly characters in the game posing in Casino Delfino, with text reading "Have a relaxing vacation!" on the bottom.