After the events of the first movie, a new villain (Dark Bowser) terrorizes the MSPT universe, looking for the Crystal Stars to give to THE ELITE to finally make His masterpiece; to be free and to create new universe in his own image.

After the events of "MSPT: The Movie", a new mysterious villain (Dark Bowser) terrorizes the MSPT universe, looking for the Crystal Stars to give to THE ELITE (A godlike creature/banished creator of the Warp Zone) to finally make His masterpiece; to be free and to create new universe in his own image. Mario has been getting visions and nightmares of this villain pretty often during and after his mission stopping Toad. Now, Mario, Sonic, and Peach have notice that time is running out... But with the help of Rosalina- Mario, Sonic, Luigi, and Tails are off seeking new and forbidden realms where the Crystal Stars are located. It's up to them to find the Stars before it's too late. Will Mario find out about Dark Bowser?—Marcus Smith