It's not an actual crossover but I'm giving it that tag anyway. This is an homage to "Phineas and Ferb" and it was written before Scootaloo's and Sweetie Belle's personalities had been defined in the show.

Applejack has to deal with an unexpected last-minute problem, so the Cutie Mark Crusaders decide to take on the very important errand of retrieving hay from another farm before they run out. Meanwhile Big Macintosh must thwart an evil pony's scheme to cause a major crop disaster and take over the tri-village area!

DISCLAIMER: I do not own the "My Little Pony" franchise or have any association whatsoever. "My Little Pony: Friendship is Magic" (c) Hasbro Studios. I do not make any money for writing this silly story, and there are no refunds for your time either.