Most popular theory:
Fluttershy was abused by her father as a filly, contributing to her shyness later in life.What actually happened:
Fluttershy was born and raised in Cloudsdale. For the first part of her life, she lived with her mother, father, and pet hummingbird. She was constantly laughed at for owning such a "weak" pet, and for not being able to fly with ease. Her trouble flying was due to a rare disease Fluttershy developed when she was three. The disease, labeled "Pegasi Poison", left Fluttershy weak and unable to walk for weeks. The doctors in Cloudsdale couldn't find a cure for the disease. Fluttershy's mother searched day and night for a cure, and tried everything from bubble baths to homemade remedies.
Meanwhile, Fluttershy's father became more and more angry. The disease that plagued Fluttershy had also claimed his mother. He remembered his mom not being able to play with him or his siblings, or do much of anything. Now, the same illness was repeating history with his only daughter. He couldn't bear to stay around the house with Fluttershy, and found himself going to bars to get drunk in order to forget his pain.
For many months, Fluttershy watched the clock as it struck two a.m. It was around this time that her dad came home and drunkenly picked fights with her mother.
Finally, after two months of not moving, Fluttershy found the strength to walk again. Her mother was overjoyed.
However, her father did not quit his now addiction to alcohol.
Fluttershy was almost immediately re-enrolled in school. But, because of her illness and time lost, she was sent back a grade. This caused all the fillies and foals to tease Fluttershy even more. Only one pony stood up for Fluttershy, and that was the overly conceited Rainbow Dash. Rainbow only stood up for Fluttershy because it made her look cool, and Fluttershy knew that. So one day, when the foals were teasing her again, Fluttershy spoke up.
"I can too fly!"
Fluttershy yelled at them.
"I'm NOT helpless! I can do things myself! And you are being VERY MEAN to me! And Fluttershy DOES NOT LIKE BEING TEASED!!"
Fluttershy got in their faces, flying a little ways off the clouds to prove her point. But suddenly, her wings faltered. Fluttershy let out a cry of surprise as she fell back on the clouds.
"Fluttershy! Fluttershy! Fluttershy can't hardly fly!"
The other ponies chanted, pointing and laughing at her.
Embarrassed beyond belief, Fluttershy ran home crying. It was then, locked in her room, that she resolved never to fight back, unless she wanted to be teased more.
"Just stay quiet, Fluttershy,"
She would whisper to herself.
"Give it a little more time, they'll forget all about you."
Fluttershy carried out her days diligently doing her schoolwork, then rushing home to her room after school. Her only real friend was Angel, her turquoise hummingbird. Fluttershy would constantly sing to Angel while doing chores or homework. Through the duration of school, the bullying and neglect her father showed towards her caused her to develop a mental illness. Fluttershy developed worsening symptoms of Multiple Personality Disorder, more formally known as Dissociative Identity Disorder (DID). Those who suffer from DID have more than one distinct personality that they can shift to at any time.
Fluttershy had three personalities:
-Shy, quiet Fluttershy,
-Assertive, bully Fluttershy,
-And insane murderous Fluttershy.
This is also why she sometimes refers to herself as "Old Fluttershy" and "New Fluttershy". Her personalities were constantly at war, trying to become her dominant person (or pony).
Fluttershy's parents started to take notice of her absence at night, and often discovered pegasi would go missing after such an event. This caused them to lock her up at night, chaining her to her bed and bolting her door shut. Fluttershy appeared at school less and less frequently, and spent many days locked in her room, singing haunting tunes to Angel. But Angel rarely got fed because Fluttershy was chained up, and therefore passed away one night. Fluttershy didn't even notice in her deranged state.
However, when Fluttershy changed back to her shy and quiet self, she became frightened of being locked in, as she had no idea why she was being isolated. She also grieved over Angel, believing her parents had to have killed her.
This is why she was so willing to leave forever when Rainbow accidentally knocked her out of the sky while racing "To defend Fluttershy's honor!". Her parents were mildly relieved as well when Fluttershy didn't come home after school, they wouldn't have to take care of her anymore.
Fluttershy discovered another life in Ponyville. She fixed up an old cottage to live in, and adopted a pure white bunny that seemed to take a liking to her. She named him Angel, after the loved pet she had lost. With the love and support of her friends, she got better, to some extent. She still switched personalities from time to time, bullying other ponies and frightening many animals with her stare. However, when she switched back she was filled with remorse and promised she would try to get better. Things are really looking up for Fluttershy, and she's finally found someplace she belongs.
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My Little Pony: The Histories
FanfictionA brief background on the characters in the popular series My Little Pony: Friendship Is Magic