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.
Daring Do is a thief trying for a second chance. Phillip Finder is a private detective with no scruples. Ponyville is a city embroiled in corruption with war on the horizon. They may be the only hope for law and order left.
Thought to have been killed as a filly, Twilight Sparkle is discovered to be returning to Canterlot. Instead of a joyous reunion awaiting her, a trail of destruction follows her as Celestia and Luna struggle to discover how, and why, she's returned.
Rainbow was always different, which wasn't a surprise, since she was the daughter of Sombra. She had unknowingly left behind traces of her magic the firstborn time she 'visited' and now the mane 6 are hunting the pony down, all expect for Rainbow.
Twilight and Rainbow have just started a new life with their newly-adopted daughter, Scootaloo, but the filly’s old parents have returned with a vengeance.