MAJOR STORY SPOILERS AHEAD. YOU HAVE BEEN WARNED.
In Fire Emblem: Three Houses, once you reach a certain point in the Black Eagles story, you will have a chance to do something that no other campaign can offer— change the story.
How to unlock the Alternative Black Eagles Story Route
Usually, at a point in the game, Edelgard will turn on you, revealing herself to be the Flame Emperor and the story will progress to the point that you will have to kill her. What you might not have realized, however, is that there are ways to change the story and turn against the Church, basically becoming the enemy instead of the hero.
To unlock the alternative path, you will need to have got your social link with Edelgard up to at least C Rank and, come 2/8 in the Calendar, you need to talk to Ederlgard while exploring the Monastery.
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There, she will talk about visiting her homeland, and you will need to choose to accompany her to start the new story path. After completing the new event and getting to the end of month mission where you will go into the Temple to face off against Edelgard through the main story, a new option will appear at the end of the mission.
After completing the Tomb event, two options will appear after beating Edelgard. Choose to Protect Edelgard instead of killing her, and the alternative route will be complete, sending you down a new path. By doing so, Flayn will leave your party, and you will side with the Empire moving forward.
This will also give you the option to romance Edelgard and become the Emperess’s wife or husband at the end of the game if you so wish.