When Sweet Apple Acres is infested by Vampire Fruit Bats, Applejack summons her friends to her property to drive them out before they destroy the entire crop. Fluttershy is reluctant to do so, citing the fact that the bats are more than simple pests and will eventually help create more apple trees due to spitting out the seeds of the apples they consume. Applejack refuses Fluttershy's idea to create a sanctuary for the bats, fearing they will destroy her entire apple supply before work is completed. Eventually, Twilight Sparkle comes up with the idea of letting the bats remain but magically removing their desire to feed on the apples.
Because the necessary spell requires the bats' full and undivided attention, Twilight asks Fluttershy to use her Stare on the bats. Reluctantly, Fluttershy agrees to the plan, not wanting to go against her friends' wishes. After gathering up all the bats in the orchard, Fluttershy uses the Stare to hold their attention and Twilight casts the spell on them. It seems to be a complete success, with the bats now refusing to eat any apples. However, the next day, Applejack discovers something is still feeding on the apples. The ponies again gather to find the culprit, and are confused when they find the bats are still not eating any of the apples. Twilight suggests a stakeout of the orchard to find who or what is eating the fruit.
That night, the friends search the orchard for any suspicious activity, failing to notice Fluttershy looking ravenously at the apples. After several run-ins with something lurking in the shadows, Applejack signals the others, who are shocked and horrified to find a bat-like Fluttershy hanging from a tree. The other ponies try to get Fluttershy (or "Flutterbat" as she is quickly dubbed) to come down, but their friend has succumbed to her feral nature and only hisses at them in response. She flies off, and the other ponies are helpless to stop her.
Twilight figures out that when she cast the spell on the bats, the magic backfired, transferring the bats' vampiric hunger for apples into Fluttershy through her Stare. While trying to find a way to return Fluttershy to her normal self, Pinkie Pie makes a comment saying they should get Fluttershy to Stare down the Flutterbat. This gives Twilight an idea, and the five ponies set a trap with Applejack's giant blue ribbon apple as bait. Flutterbat is attracted by the scent of the juice, but when she tries to pounce, the others hold mirrors on her, forcing her Stare on herself. While she is distracted, Twilight casts a counter-spell, seemingly returning Fluttershy to her normal self.
Later, Applejack and the others build the sanctuary Fluttershy had requested for the bats, having learned that the quickest solution to a problem isn't always the best solution. Fluttershy also learns not to cave in to peer pressure, and to not be afraid to speak up when you don't agree with your friends' actions. However, no one notices that Fluttershy still has her vampire fangs...
The Viking Alliance