After a portal incident, Johnny, his sisters and Dukey landed in Ponyville and they've been turned into ponies! They also meet the Mane 6. Little to know, that Johnny's allies were also brought here as well! Suddenly, Queen Chrysalis returns and she even teamed up with Wacko and the others! Now the gang has to go on various adventures, stop the evil and find a way home as well!

Sonic and Tails meet a boy/dog duo from a different world, who called themselves as Johnny and Dukey. Meanwhile, a fairy, named Luna, brought the heroes to a quest, to collect the Super Crystals. However, Eggman teamed up with Johnny's villains for world domination and they have Scourge in the team! So it's up to Sonic, Johnny and their friends to save their worlds from the darknes

While trying to get the Master Emerald and save Cream from Dr. Eggman, Sonic and Friends are transported to a new world called "Porkbelly" where they meet Johnny, his sisters and his dog anwhile, Eggman teamed up with Wacko and others, to taking over both worlds with their DOOM-Blaster. So it's up to Sonic, Johnny and the gang to save the world and stop them!