In Luna Eclipsed, My little pony Fluttershy sequesters herself at home in her cottage during Nightmare Night, and refuses to answer the door until she learns that her visitor is Twilight. She is then forcibly brought out by Twilight to give Princess Luna a lesson in how to speak softly, with the Princess's "Royal Canterlot Voice" terrifying her.
In Putting Your Hoof Down, My little pony Fluttershy becomes "assertive" after attending a seminar from Iron Will. However, when she over-asserts herself, (e.g. going berserk when a mail carrier delivers her the wrong mail), Rarity and Pinkie attempt to intervene. In the end, she realizes her mistake after driving her friends away in tears, and with the help of her animal friends, locks herself in her cottage to prevent herself from causing anyone more harm.
When Iron Will visits shortly afterwards to collect the fee for his seminar, My little pony Fluttershy uncharacteristically politely refuses him, eliciting shock from the onlooking Rarity and Pinkie Pie. She explains that she is evoking Iron Will's earlier guarantee that if a customer was not satisfied with his services, they would pay nothing; as she is not satisfied, she will not pay him. Iron Will relents and leaves, and her friends congratulate her on her newfound confidence.
In Dragon Quest, she again displays her fear of dragons. My little pony Fluttershy pointedly refuses to watch the Dragon Migration with her friends, despite Twilight's coaxing. It culminates in My little pony Fluttershy pushing past Rainbow Dash and jumping out the window, fleeing the scene before any of them could follow her..
In Hurricane My little pony Fluttershy, she tries to evade her responsibilities as a Pegasus to help create a tornado to move water to Cloudsdale from Ponyville's reservoir. After some insistence from Rainbow Dash, she reveals that she is afraid of humiliating herself by performing badly as a flyer in front of all the other Pegasi. She becomes even more discouraged after the anemometer (wingpower gauging machine) gives her wingpower as only 0.5. Her animals' motivation causes her to engage in a period of training and exercise, but her second attempt only puts her at 2.3, further diminishing her hopes for improvement. In the end, Twilight convinces her to help when the other Pegasi's wingpower proves not to be enough to create the tornado. With a sudden burst of determination, she manages to surpass all the other Pegasi in flying speed, completing the 800 wingpower minimum to create the tornado and resulting in the water successfully reaching Cloudsdale.