Sunny Starscout owns a Fluttershy figurine that she plays with. Under the control of Sunny, Fluttershy excitedly runs along with her friends to an adventure. She later asks Twilight Sparkle if a foe they're going to face is scary. She proclaims that she will spread hugs alongside her friends. She is scared and runs away from Rarity (under Sprout's control) attacking the others.
Through the reign of Twilight Sparkle, Fluttershy remained in Ponyville, but would regularly venture to Canterlot to provide consultation to the Princess. She operated an animal sanctuary in Ponyville with her good friend Discord. The two taught young Ponies about the virtue of Kindness and maintaining the natural world.
One day, a now middle-aged Fluttershy was shopping at Ponyville's marketplace. She was rudely cut in line by a mysterious Alicorn. When Fluttershy protested the gesture, the Alicorn coldly dismissed her and violently knocked her to the ground. Fluttershy recovered from the event, but the Alicorn's malicious deeds across Equestria continued to negatively impact her. The Alicorn's lies and bullying caused great distrust and conflict between the Pony kinds which caused the parents of her students to forbid them from attending her sessions.
Fluttershy participated in an obscure battle that temporarily defeated the Alicorn. However, sometime later she disappeared from Equestria along with the rest of the Mane 6. Her legacy would be kept alive by Discord, as he continued to be a caretaker to a number of animals in the now abandoned Canterlot.