Princess Celestia senses that there is another crystal empire somewhere above Canterlot. So she went outside and saw what appears to be King Sombra's crystal castle that is in the sky above the clouds. So she calls the Mane 6 and Luna so they can work together to stop Sombra once again. Before the can reach the castle, they must defeat Queen Chrysalis and King Bowser. Celestia orders the Mane 6 to step back and let her fight the Changeling Queen and the Koopa King. She calls out Mario as her partner so the battle can be two on two.