After a late start, Spike, Fluttershy, and Pinkie Pie are left behind as Applejack, Twilight, Rarity, and Rainbow Dash catch the train to Canterlot. Pinkie suggests to go into the library and take Twilight's spare chariot in the lab. When the three uncover the peculiar looking chariot, and find a weird drink next to it. After convincing Fluttershy to drink it, the three fly in the chariot, only for Fluttershy to go unbelievably fast. The next thing they know, they're somewhere else, somewhere cold, primitive, oddly familar. Can these three get...well, back to the future without messing up history?

Pinkie Pie, "Hey Fluttershy, you gotta back this thing up, we don't have enough road to get to 88."

Fluttershy, "Roads?" She stopped to think for a moment. "I'm a pegasus, I've never needed roads."

The chaotic nature of the chaos emeralds had been strong enough to reawakened a past evil in Equestria. Sonic had fallen from the sky only to wake up in a strange library talking to a purple dragon. However, Sonic was not the only one to cross into Equestria. Eggman wakes up in a strange throne room in the middle of a forest hearing voices of a regal and sinister voice calling out to him. And Discord laughs manically as he uncovers a large gem filled with chaotic energy. Can Sonic, Twilight, and the rest of the wielders of the Elements of Harmony stop Discord from ruling all of Equestria?