When the Friendship Festival is crashed by the Storm King's forces, Twilight is saved by some creature, and along with her friends, they are forced from Canterlot. Now, they must find a mysterious queen and find a way to save Equestria again.
Sonic, the CMCs, and Spike teams up with their new allies to get the emerald before Robotnik and Knuckles while the Rainbooms investigates the Dazzlings' latest scheme in Hoovaii.
After the two groups meet up due to circumstances, Sonic and the Equestria Girls must team up to defeat an evil genius, who wants to use his power for world domination, while on the run from the government lead by a special agent.