While running through Green Hill Zone, Sonic and his friends are sent into Equestria thanks to another scheme by Eggman. There he meets the bearers of the Elements of Harmony, and with their help, as well as his own friends, Sonic will have to stop Eggman's schemes yet again.

But what will happen when the seven Chaos Emeralds, objects of pure chaos, are brought into this world? Will Equestria be torn by uncontrollable chaos? Only time will tell.