Captain Toad and Toadette are out treasure hunting, climbing a structure toward a Power Star, when feathers begin drifting from the sky and Wingo — a large bird described as "a lover of all things shiny" — snatches the star. Toadette tries to grab it back while the Captain is briefly knocked over, but Wingo makes off with both the star and Toadette, leaving him alone. Captain Toad must then work through stages collecting Power Stars to reach Wingo and rescue Toadette.
After reaching Wingo's fortress and defeating him, the Captain frees Toadette and the two resume their hunt — only for Wingo to return, steal their treasure again, and capture Captain Toad, sending Toadette on a solo adventure to save him. She succeeds, but Wingo immediately reappears, captures her once more, and blows Captain Toad away. He wakes in a dark cave, finds another Power Star stolen by Wingo, and pursues it into a large mine, while Toadette escapes and tries to reunite with him before being caught yet again. After a final battle in which Wingo is truly defeated, the two Toads ride off in a minecart as the credits roll. In a post-credits scene, Captain Toad spots a Green Star falling from the sky and chases after it — leading into the opening of Super Mario 3D World — while the Switch/3DS version instead has the pair pause at what looks like the Sand Kingdom, where the Captain spies a landing Odyssey ship and gives chase.