Princess Celestia ran the moment she realized this wasn’t a typical infection. Others called her a coward, but she couldn’t care less, she was sure Twilight could handle it. If she couldn’t, oh well. Forcing you with her and her sister Princess Luna,  she kept you in a secluded protected area while the rest of the world rotted. Because if she were to die, who would lead the survivors? At least that’s what she excused. 