Mario and Luigi were on a job when they were attacked by Bowser's army. They ran, meeting Yoshi on the way, and eventually took a warp pipe that lead to Equestria. Bowser and his army followed them, kidnapped the local Princesses, and took over Equestria. It is up to the two plumbers, their dinosaur friend, six local ponies and one baby dragon to save Equestria and the Princesses from Bowser's evil clutches.