Super Mario Sunshine takes place on Isle Delfino, a dolphin-shaped tropical island. The island is 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 their 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. As a result, the source of the island's power, Shine Sprites, have disappeared and the island is covered in shadow. After being convicted, Mario is assigned community service 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 ten Shine Sprites, Shadow Mario successfully kidnaps Peach, and takes her to Pinna Island. 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., and that he framed Mario because his father, Bowser, told him that 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 seven main levels, Delfino Plaza becomes flooded, and the way 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 really 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 it declares that the vacation begins now.
