After the time of Mario & Luigi: Paper Jam, a new book has been discovered, filled with dark magic, which put the entire mushroom kingdom at risk. Unfortunately, word spead, and soon enough, every Toad knew, but so did all of Bowser's Minions. Now, with no one to rule them, they were free to do anything at last, which meant directly disobeying what Bowser would say (had he still been here) and go fetch that book. The minions sent the Elita Koopa Force to fetch the book. They succeeded, and used it to warp the mushroom kingdom and everyone in it to a corrupted version of their past, including Mario.

Now, join Mario as he stops the Elite Koopa Force, save the mushroom kingdom, and prevents the re-birth of Bowser.