Risky Boots and Baikinman has finally kidnapped the half genie Shantae and made a plan to threaten all Yoshi species into extinction by killing the Yoshis and taking all the resources by sending an army of Tinkerbats and Kabirunrun. The remaining Yoshis (Green, Red, Blue and Yellow) needs help from Mario and Friends (Mario, Luigi, Peach and Toads), Anpanman and Friends (Anpanman, Currypanman, Shokupanman, Uncle Jam, Batako and Cheese) and three of Shantae's friends (Sky, Rottytops and Bolo) to stop the demise of Yoshi's Island as well as the Yoshi Kingdom. Will they stop the Yoshi extinction and save Shantae?