Super Mario Sunshine
Mario, Peach, Toadsworth, and a few other Toads were on lounging vacation toward Isle Delfino. Peach noticed a mysterious figure resembling Mario on the plane's video advertisement, but doesn't get her words through to the two men. The Toad Express then took an abrupt stop as the Delfino Airstrip seemed to be overrun by an icky paint-like goop that's moving. Mario moved ahead and discovered the F.L.U.D.D., the Flash Liquidizer Ultra Dousing Device.
After ridding the airstrip's search of this paint and receiving a Shine Sprite, Mario is arrested by the Isle Delfino authorities. Apparently, Mario had been responsible for having vandalized the island, which scattered its Shine Sprites, and cloaked the island in darkness. Charged with community service, Mario now had to return Isle Delfino to its former way of life.
During community service, this mysterious Mario figure ended up kidnapping Peach and, after having followed him to Pinna Park, turned out to have been Bowser Jr., the son of King Bowser himself. He's being led to believe that Peach is Junior's mother by Bowser, and has decided to "return Mama Peach" all the while masquerading as "Shadow Mario" to get the real Mario sent to prison.
A flood on Delfino Plaza allowed Mario to follow Shadow Mario into Corona Mountain. Having climbed up the mountain, Mario landed on a giant stone bowl of green water, with Bowser, Bowser Jr., and Peach drifting inside of it. After breaking the bowl, everyone fell down onto Isle Delfino. Mario spotted F.L.U.D.D. to have broken down during the encounter, but he's fine after a few repairs hours later. In the meantime, Bowser Jr. confessed he didn't really believe Peach was his mother, but wanted to fight Mario again when he's older, Bowser being proud of him before enjoying their vacation.
- Mario and Princess Peach meet Bowser Jr. for the first time, placing this before all other games featuring Mario interacting with Bowser Jr.
- This game takes place after Luigi's Mansion, as it is referenced by a Pianta in Hotel Delfino.
- Likely takes place during a time period in which King Boo has been captured as a fake King Boo was created by Bowser Jr. during this game.
- Mario is famous enough to be known on Isle Delfino at this point, but it’s his first time visiting the island, placing this game before all future Delfino appearances in the series.
- The F.L.U.D.D. appears to be a downsized version of the Hydrogush 4000 from Mario & Luigi: Partners in Time, indicating that this game takes place after that.
- F.L.U.D.D's scan of Mario mentions that his least favorite food is Poison Mushrooms, implying that Mario ingested one previously. This likely places this title after the events of Mario & Luigi: Superstar Saga + Bowser's Minions, where Mario accidentally eats a Poison Mushroom and develops Bean Fever
- Theory: Delfino Plaza's Flood cleared up the Graffiti
- Theory: Power Moons and Shine Sprites and Power Stars
- Theory: Sunshine King Boo's Identity
- Theory: What is Goo