Perhaps a plot where a Jedi, disillusioned with the Clone Wars, turns to the Sith Empire in the hope of finding a different solution to the galactic conflict. But once there, they realize the true evil of the Sith and have to fight their way out, all while being hunted by both the Sith and the Jedi who now consider them a traitor.
Another idea is that the Sith Empire decides to use a new form of Sith magic during the Clone Wars. This magic starts to corrupt the planets it is used on, and the Jedi have to find a way to stop it. The story could show the different reactions of various species to this new threat. For example, some might be more susceptible to the corruption while others are more resistant. The Jedi would have to form alliances with these different species to combat the Sith Empire's new weapon. This would involve a lot of political maneuvering as well as physical battles. It could also explore the nature of the Force and how the Sith's use of it in this new way affects the balance.
One plot idea could be a Sith Pureblood rising through the ranks in the Sith hierarchy during the Clone Wars. They might start as an apprentice and have to prove themselves by undertaking dangerous missions against the Jedi. For example, they could be tasked with infiltrating a Jedi stronghold to steal a valuable artifact. Another idea is a story about a Sith Pureblood who has a change of heart and tries to defect from the Sith. This would involve a lot of internal struggle as they fight against their dark side training and the fear of reprisal from the Sith Lords. A third plot could revolve around a group of Sith Purebloods who form a secret society within the Sith order, with their own goals and agendas that may or may not align with the overall Sith plans during the Clone Wars.
A possible fanfiction could focus on a group of clones who discover a hidden Sith Empire base during the Clone Wars. They have to fight against the Sith's dark powers and their own programming as they try to warn the Republic. This could involve intense battles and moral dilemmas for the clones.
In a fanfiction where the Sith Empire prevails in Star Wars Clone Wars, the galaxy would be a very dark place. The Sith values of power through domination would mean the subjugation of countless species. Jedi would be either wiped out or forced into hiding. The very fabric of the Force might be warped as the Sith use it for their evil ends, like enslaving planets through dark side magic. It could also lead to a new hierarchy in the galaxy, with Sith Lords ruling over sectors, and any form of democracy or freedom would be a distant memory.
The rise of the Sith Empire in Clone Wars fanfiction could start with a series of strategic moves. The Sith might have infiltrated key positions within the Republic long before the Clone Wars even began. They could have manipulated the creation of the clone army, for example, ensuring that they had a way to create chaos and further their own goals. Once the war started, they could have gradually turned the tides in their favor by making secret alliances with certain separatist groups and using their dark side powers to influence key battles.
A possible story idea could be that your OC Sith discovers an ancient Sith prophecy. They believe it will lead them to ultimate power. So, they start a quest to find the artifacts related to this prophecy during the Clone Wars. This could involve them infiltrating Jedi strongholds and causing chaos.
A great plot for Star Wars The Clone Wars fanfiction could be centered around a new, unknown planet that gets caught in the middle of the war. The planet has its own unique species and culture. The story could follow how the clone troopers and the Jedi interact with this new civilization, whether they try to protect it or use it for their own strategic advantages. Or perhaps a story where a group of clone troopers start to develop their own individual personalities and question their loyalty to the Republic due to some unethical orders they receive. This could lead to a conflict within the clone ranks and force the Jedi to take sides.
Well, a great storyline could involve an OC Sith who was once a Jedi padawan but was seduced by the dark side. In 'Star Wars The Clone Wars', this character could be on a journey to destroy their former Jedi friends while also dealing with the internal conflict of their new Sith identity. They may struggle with memories of their Jedi training and the relationships they had before turning to the dark side.
A great plot idea would be to have a story centered around a group of younglings who are accidentally caught in the crossfire of a Clone Wars battle. They have to rely on their basic Jedi training and the help of some friendly clone troopers to survive. As they journey through the war - torn landscape, they grow and learn more about the reality of the war. Also, a story about a Separatist scientist who has a change of heart and tries to defect to the Republic with valuable information about new droid technology could be really interesting. He has to avoid being hunted down by his former allies while trying to make his way to the Republic lines.
One interesting plot idea could be exploring the backstory of the Ones on Mortis in more detail. Maybe a young Jedi discovers a hidden prophecy about Mortis and goes on a quest to understand it. This could involve facing challenges related to the balance of the Force that Mortis represents.
A great plot might be Katooni having to deal with a dark side - influenced Jedi who has turned against the Order. She has to find a way to either bring this Jedi back to the light or stop them from causing too much harm. Also, perhaps a story where she discovers an ancient Jedi artifact that holds the key to a great power, and she has to protect it from both the Separatists and those within the Republic who might misuse it.