A strange increase in animal attacks have occurred in and around Ponyville, and everytime afterwards, Fluttershy would be there to "offer help". She would then track down and make sure that said animal would never attack again, and receive "donations" for her good deed. One day, a private citizen of Ponyville (Who's name has been withheld for their protection) felt suspicious about this and decided to investigate further. They visited Fluttershy's cottage and reported sighting of many of the Animals who had previously caused trouble loitering around, with Fluttershy opening the door carrying a golden emerald broch that looked way too expensive for her to afford, given her income. Sensing that foul play was at hoof, the good Samaritan reported it to the local police and the next day, dispatched detectives to her cottage. When they questioned her about the emerald broach, she said "oh this? I don't know where it came from. It was on my nightstand one morning and I have no idea where it came from. I think maybe Angel Bunny found it and put it there. He certainly is a sweet thing."

Then the detectives felt a little suspicious, as they received a report two weeks ago from Canterlot about a gang of bunny burglars breaking into a jewelry store at night and stealing half of the merchandise plus some bits. Receiving a warrant from the judge and with several officers backing them up, the detectives returned to Fluttershy's cottage to conduct a search. They found no other pieces of jewelry that were reported stolen. They did however find 1000 bits sitting in one of her closets, Along with a half filled application for a building permit for what Fluttershy says is for an animal sanctuary she was building. But detectives weren't buying it. They decided to take her down to the station for further questioning. They asked her where she was two weeks ago, and she said in Canterlot helping her friend Rarity out with some menial tasks at her boutique, which would put her in the vicinity of the jewelry store that was robbed.

Continuing their investigation, detectives gathered witnesses who reported seeing Fluttershy speak to a group of suspicious looking rabbits that fit the description of the ones who robbed the jewelry store. Seeing as how Fluttershy has the ability to speak with animals, detectives concluded that she was not only the ringleader of the robbery, but also involved in a racketeering operation to extract money from citizens in exchange for protection from animal attacks. The detectives submitted their findings to the district attorney and Fluttershy was charged with robbery and racketeering. Fluttershy panicking over this tried to explain herself despite being read her rights, but all she did was unintentionally incriminate herself.

The DA eventually worked out a very generous plea deal no way out, Fluttershy was forced to sign a plea agreement and was sentenced to 3.5 years incarceration and was shipped out to Foalsom Prison, about two hundred miles away from her home. Upon her arrival though, the administration deemed that she would not do well in gen pop due to her timidness and naivity. So for her own safety, she was placed in Solitary Confinement fot over a year of her sentence before having her security level and downgraded and transfered to a low security facility.