This is what I think happened in the original timeline:
- The Grand Duke seized the influence of the Emperor and held onto all the power in the Government, since the Duke didn't care for politics because of the war
- Grand Duke and Princess managed to keep the Emporor and his Sister away from one another with lies and constantly suppressing/humiliating his sister
- Nobles embezzled and grew currupt while lying and blaming the Emperor for the Empire's decline
- Grand Duke and Princess hatch a plan to get rid of the country bumpkin duo (Emperor and Sister), they instigate the people and nobles to rebel by justifying it, by saying, that the Emperor is a Tyrant and must be removed from power
- The Grand Duke wants power and the Princess wants the Duke so they staged all the events that happened in the story
- To gain military power and to keep the lineage "pure" the Grand Duke and the Princess tricked the Duke into marrying the Princess, and used his influence to purge the Empire of it's "Tyrant" Emperor and corrupt nobles. They killed Alicia because she knew to much and to avoid any future hassles (but they probably just thought of her as an eyesore)
- And they all lived happily ever after, the end!
Basically the Emperor was a puppet they thought as lowborn, who mas manipulated, used, thrown away. His sister was just a hassle they never even put her in their eyes and she was also powerless to help her brother.