Goin' Quackers begins with Donald Duck, Gladstone Gander, and Gyro Gearloose watching television reporter Daisy Duck discovering the mysterious temple of the evil magician Merlock. As she tells the story, Merlock discovers Daisy and kidnaps her. His arch rival Gladstone sets out to find her before Donald, who decides to use Gyro's new invention, the "Tubal Teleport System", to track down Merlock and Daisy. However, a piece of Gyro's device is missing, and to get the machine working again, Donald must go on a journey to recover it. Along the way, he must compete with Gladstone, reverse the spells that Merlock put on Huey, Dewey, and Louie's toys, and defeat several bosses, including the Beagle Boys and Magica De Spell.