When Trixie is hospitalized with amnesia, there are only six ponies up to the task of bringing Trixie back. To bad the mare is absolutely terrified of them.
The Alicorn Amulet tainted Trixie. Over time, she recovered, yet it haunts her still. Exploring Equestria, Trixie is determined to finally achieve Greatness and true power, no matter what. In Phantasia, a mare shall defy destiny.
After Tirek's defeat, magic was restored to everypony who it had been taken from - except Trixie. Now, injured and facing months of reduced magic, Trixie has to hang up the hat and cape, or risk destroying her healing horn forever. Hilarity Ensues.
Trixie continues on to Las Pegasus, learning more on what it means to be an Alicorn. Discord must track down Fluttershy before she succumbs to her new instincts, and Twilight must learn to balance her duties and interest in a certain showmare.
Bad things happen. It's a fact that Trixie has accepted. A bitter fact, true, but a fact nonetheless. But transported into another world out of the blue might seem a bit too much, she thinks.