- Mario must travel to worlds unknown in order to stop Bowser from marrying Princess Peach.
- The game begins in the middle of a battle, and a rather familiar one at that. In the skies above Peach's Castle, Bowser has captured the princess and taken her onto his ship. But Mario is quick enough to board the ship immediately this time, and he attacks Bowser with all he's got. Unfortunately for Mario, Bowser has a secret weapon: His hat, which functions as a boomerang and catches Mario off-guard. Unable to react, Mario is knocked off the ship, and Bowser flies away in his airship.
Mario fall for a long time, and lands in Bonneton, a small town in the Cap Kingdom, populated by small, hat-shaped ghosts. Bonneton has been attacked by Bowser and his minions, and all their airships has been destroyed. One of the ghosts, named Cappy, greets Mario, and offers to help him free Peach from Bowsers grasp. Cappy's sister has been abducted as well, and the two form a partnership, in which Cappy functions as Mario's new cap. Armed with his new ally, Mario enters the large tower in Bonneton, and learns about Cappy's signature ability: He can possess other creatures. With this newfound power, Mario climbs the tower as a frog, and gets to the very top, where he meets Bowsers wedding planners; The Broodals, a rabbit family. Mario defeats one of them, called Topper, and captures (possesses) an electric Pylon, which lets him travel along the power lines to the next kingdom.
Mario rides the power line all the way to Fossil Falls, an idyllic cliff in the Cascade Kingdom. There, Mario finds an old airship, called the Odyssey, and attempts to start it, with no success. He then learns that the Powermoons scattered around the area can power the Odyssey, and he starts collecting some. His quest is interrupted by Madam Broode, the mother of the Broodals and a vicious old lady. Mario defeats her by possessing her pet Chain-Chomp, and uses her Powermoon necklace to power the Odyssey. With the ship active, Mario and Cappy then sails to the Sand Kingdom, to a small town called Tostarena, populated by small friendly skeletons. Tostarena is currently in a frozen state despite being in a desert, and Mario first defeats another Broodal, Harriet, before heading underground and battling Knucklotec, a giant ice monster. Defeating him makes the town warm again, and after collecting enough moons to power the odyssey again, Mario and Cappy sail to their next target. They were too late to catch Bowser in Tostarena, and Bowser is slowly building up his wedding with stuff he takes from They were too late to catch Bowser in Tostarena though, and Bowser is slowly building up his wedding with stuff he takes from the different kingdoms. After Tostarena, the player have two options on where to go, even though they have to visit both anyway. Mario and Cappy goes to the Lake Kingdom, a calm and mermaid-filled lake, and defeats Rango the Broodal, but are too late to stop Bowser from stealing a wedding dress. They also of to the Wooden Kingdom, a tree-filled mountain that also has a power station and a flower garden. Mario and Cappy defeats a flower-stealing UFO, and beats Spewart the Broodal, but once again fail to stop Bowser from stealing what he wants, this time a bouquet of flowers.
After the first four Kingdoms, the next stop is the Metro Kingdom, a large city. However, before Mario and Cappy get there, they are interrupted by Bowser, who challenges Mario to a duel in the skies. Mario wins, but Bowser fires his cannons and blows the Odyssey out of the air. Mario and Cappy and in the Lost Kingdom, a tropical island in the middle of nowhere. After a brief fight with Klepto the hat-stealing bird, they gather enough moons to repair the Odyssey and continue their hunt.
They arrive in Metro Kingdom only to find it dark and filled with monsters. After climbing the tallest skyscraper in the city, Mario and Cappy defeat Mechawiggler, an energy-leaching robot monster. After that, the city returns to normal, and starts to prepare for their annual festival. Mario helps the mayor with gathering a band and securing the city's power plant, and when everything is ready he takes part in the festival, where he receives 3 power-moons as thanks. After gathering the rest of the moons needed, our duo sails onwards, to another fork in the road. They visit the Snow Kingdom, where they cleans up the mess left by Bowser, defeats Rango again, and participates in the annual Bound Bowl Grand Prix. They also visit the Seaside Kingdom, an idyllic beach ruined by a giant monster drinking all the Sparkly Water the inhabitants are so proud of. After defeating the monster and collecting enough moons, they travel to the Luncheon Kingdom, a volcano and a little town, both filled with food and food related items. Our heroes defeat Spewart again, before engaging in a battle with a monstrous bird in order to save the carefully prepared food in the giant soup bowl that is the central attraction of the kingdom.
After the Luncheon Kingdom, they head towards Bowser's Kingdom, only to once again meet him in the skies. And once again, Bowser shoots them out of the sky, this time with the help of a giant thunder-breathing dragon. Mario and Cappy lands in the Ruined kingdom, a dark, broken castle, and takes down the dragon, before taking off again. They reach Bowsers Kingdom, and after climbing the steps and scaling the walls, they reach Bowser at the top, only for him to fly away once again, this time to the moon. Our heroes are kept from following him at first, due to a giant robot appearing. It's powered by the four Broodals, and a climactic fight ensues. After defeating the Broodals, the main duo sails to the moon, and after navigating a lava-filled cave deep underground, they reach the church where Bowser is planning to marry peach. Mario storms in, but is caught by bowser and dropped through a trapdoor in the floor. Mario lands on a big plateau, and Bowser jumps down to finish him, and so begins the final battle, in which Mario and Bowser both use their hats to a large degree. After defeating Bowser, Mario runs towards Peach, but the cave collapses and sends all three of them down into the core of the moon. There, Mario possess Bowser, and carries Peach through a collapsing cave. They escape in the last second, and all land safely on the moon. Mario walks towards Peach with a flower, but Bowser has the same idea, and they have a little quarrel, which ends with Peach rejecting them both and climbing aboard the Odyssey. Mario comforts Bowser a little, before running towards the Odyssey and just at the last second grabbing on to it, bringing up the title card one last time.
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