In a parallel world where dinosaurs evolved into intelligent beings, Brooklyn plumbers Mario and Luigi stumble into a hidden dimension. They come across a mysterious woman named Daisy who is abducted by henchmen from this alternate universe. The brothers discover that Daisy is the key to solving an ancient mystery and the portal to this other world is located beneath the streets of New York. Determined to rescue her, they follow her captors into the dystopian realm ruled by the tyrannical King Koopa. This world is vastly different from their own, marked by advanced yet decaying technology, strange creatures, and a populace living in fear under Koopa's dictatorship.

As Mario and Luigi navigate the dangerous terrain, they encounter a variety of odd and hostile inhabitants, including Koopa's loyal underlings who are out to stop them. They find allies among the oppressed citizens who wish to overthrow Koopa's regime. Utilizing their plumbing skills and newfound gadgets from this alternate universe, the brothers face numerous obstacles in their quest to save Daisy and thwart Koopa's plans for domination. Along the way, they uncover the deeper history behind Daisy's lineage and the true extent of Koopa's evil intent, leading them to a climactic showdown that will determine the fate of both worlds.