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Fluttershy and the Rainbow Factory is an ongoing fancomic developed by Deviantartist The1King. The story revolves around the Mane 6 touring the mysterious Rainbow Factory.
The comic itself can be found HERE
The cover for the story was first released on August 25, 2013. So it is likely this takes place sometime between seasons 3 and 4 or sometime during season 4 as Twilight is an alicorn and the library is still standing.
Chapter 1: The story begins at the library where Twilight, Applejack, Rarity, Pinkie Pie, and Fluttershy are preparing to meet up with Rainbow Dash at the factory where the manager has offered a tour to end all the rumors. Fluttershy, all to aware of the stories, warns about the Factory. Everypony however doesn't believe her, much to her dismay.
The story then cuts to the girls arriving at the Factory in the hot air balloon. As Twilight applies the cloud walking spell, the others attempt to pull a stubborn Fluttershy of the balloon. Just as they finally tie her up with AJ's rope the factory gates open, revealing the manager as Rainbow Dash herself, which leads Fluttershy to a near emotional breakdown. After Rainbow tries to calm her down, she leads them into the factory where the 5 are shown to the Rainbow Room, just as Rainbow Dash begins singing a parody of 'Pure Immagination'. As the song ends Fluttershy catches a glimpse of Dash's eye and sees it become strange for a brief moment, leaving Fluttershy stunned.
The 6 are then quickly introduced to the Aappa Lossas (an obvious parody of Oompa Loompas), short stallion-like ponies with an orange coat and a green mane. Rainbow Dash explains they come from a hostle place called Lossa Land, to which Twilight tries to push that there is no such place only to have Rainbow Dash dismiss her. Fluttershy, feeling sympathetic, picks up one of the Aappa Lossas only to have it scare her causing her to knock Rarity into the Rainbow river. After a failed attempt to pull her out Rarity is sucked up one of the pipes in the river. Rainbow Dash says she is being sent to the 'Cloud Stuffing Room', and tells a crying Fluttershy that "She'll be just fine."
Chapter 2: The story continues with Rarity continuing her journey though the pipes where she is shot out the other end. She falls briefly, only to be caught by a large net. She thanks whoever caught her, only to reveal a strange character coming out of the darkness, leaving Rarity with a concerned look on her face.
The next page shows her tied up in a rope, possibly being dragged. When she tries to use her magic a drilling device come down and shaves off her horn, the figure, now revealed to be BronyDanceParty, welcomes her to the real Rainbow Factory.
It should be noted that the author tends to leave his readers on a cliffhanger with each post.
Since its release the comic has retained a growing following among fans of MLP, Rainbow Factory, and Willy Wonka.
As the story continues to progress many viewers came up with their own theories on certain scenes and what the secret of the factory really is.