As a filly, Twilight Sparkle had a very serious arcane burst, thus never really recovered well from the magical incident. In fear that another arcane burst may occur, Princess Celestia had come to a decision that in order to prevent a horrible incident again, the unicorn must go through a life-risking process:

Surgery.

Removing Twilight's magical horn seems the only way to prevent the arcane bursts from happening again. The rest of the Elements of Harmony are worried, however, for that they are unsure if, since Twilight is the Element of Magic, this surgery will render the Elements useless? Even Princess Celestia herself is concerned about the future of the Mane Six, and the fate of Equestria. Maybe, perhaps there is something that is more stable for Twilight to use her magic with?