After his so-called reformation, Discord longs for revenge on the Spirits of Harmony. So when he is visited by Dr. Eggman, offering revenge on his enemies in exchange for partnership, he jumps at the chance. Now the heroes from both worlds work together to bring both villains down as they try to collect all the chaos emeralds... and destroy the Elements of Harmony once and for all.

But maybe fate brought these two worlds together for a greater reason. Each Spirit of Harmony has a bond with one of the Sonic Heroes, the greatest of all between Sonic and Rainbow Dash. With both Chaos Control and Friendship, both worlds combined would be unstoppable. Unfortunately, the same may be said for the enemy.

This is the constant struggle between Chaos and Harmony opened up to a whole new level.