Pinkie goes to Zecora's house and notices that Zecora's sister is brewing Zecora up. Now Pinkie Leaves and warns the others. First they have to get Zecora out of the Brew. Then they must travel all of Equestria to get special ingredients to heal Zecora. That doesn't mean there aren't epic battles like fighting Gilda. You have to travel to places like Clousdale, Canterlot and more before Zecora says good-bye.
You get to make your own pony in the game. You can choose to be a Pony, Baby Dragon, Teenage Dragon or a Zebra. Each Race gets different Missions. But in order to choose your race and make your own characters you have to beat the Mane 6's Stories. So the Missions are hard a bit.
Missions are done from one city to another. So for example Ponyville first.
Zecora Quest: Go save Zecora
Sister VS Twilight: Defeat Zecori Prequest: Zecora Quest
Collectorship: Talk to Zecora Prequest: Sister VS Twilight
Poison Joke: Collect 20 Leaves of Poison Joke Prequest: Collectorship
Diamond Crown: Collect 5 Cut Diamonds Prequest: Poison Joke
Final Gold: Search the Everfree Forest for 3 Dragon Gold Items Prequest: Diamond Crown
Dragons Again?: Defeat the Teenage Dragon Gang Prequest: Final Gold
-Rainbow Dash and Fluttershy Go to Clousdale-
Angry Cockatrice: Collect 1 Cockatrice Feather Prequest: Dragons Again