Daylight

Nearly a century later, Celestia and Twilight have formed a hidden relationship over the decades. Though it soon comes crumbling down went the Canterlot nobility begin to shun same gender couples. Finally the distaste becomes too apparent and the time comes for Celestia to make the tough decision of sending Twilight away for the protection of her throne.

Warning: This is a Twilestia ship so it might not agree with your personal ships and it is GirlxGirl. As well there will be several mentions of homophobia so be warned.