One idea could be exploring the backstories of the clone troopers in more depth. For example, showing how they interacted during their training and formed unique bonds. Another could be a story about a Jedi Padawan who gets separated from their master during a battle and has to find their way back while facing unexpected challenges. A third idea is to create a story where a group of clones discovers a hidden Sith artifact and has to decide what to do with it.
An interesting plot for Star Wars The Clone Wars fan fiction could be about a youngling who stows away on a clone ship. As they travel with the clones, they learn about war and the ways of the soldiers. The youngling could also have a special connection to the Force that helps the clones in unexpected ways. Another plot could involve a Sith apprentice who is sent on a secret mission during the Clone Wars. This mission could involve infiltrating the Jedi Order or finding a powerful ancient relic. And a third option could be a story about a droid that gains sentience during the Clone Wars and tries to find its place in the conflict, whether it's helping the Republic, the Separatists, or trying to stop the war altogether.
One plot idea could be Boba Fett teaming up with a young Jedi who is on the run from the Separatists. They start off as enemies but gradually realize they have a common goal of uncovering a Sith plot. This would show Boba Fett's complex character as he has to decide between his bounty hunting instincts and doing the right thing.
One idea could be focusing on a young clone trooper who discovers he has unique Force abilities. He then has to hide this from his superiors while trying to figure out what it means.
One idea could be exploring the backstories of the clone troopers in more detail. Maybe focus on a particular clone and his relationships with his brothers. Another could be creating a new adventure for Anakin Skywalker during the Clone Wars that wasn't shown in the original series. For example, he could be sent on a secret mission to a planet that has a powerful and ancient Sith artifact.
She could be a clone who rebels against the clone programming. Instead of blindly following orders, she starts to question the morality of the Clone Wars. She might try to find a way to end the war peacefully, even if it means going against her own side. This would create a lot of internal conflict as well as external conflict with her superiors and comrades.
One interesting plot idea could be exploring Dooku's early days in the Sith. Maybe showing how he was gradually corrupted by Sidious. Another could be a story where Dooku has a change of heart briefly and tries to make amends in some small way during the Clone Wars, but is quickly pulled back into the dark side by Sidious' influence. A third idea could be a fanfic that focuses on Dooku's relationship with his former Jedi colleagues during the Clone Wars, like how he feels when facing them in battle.
A plot idea could be a story from the perspective of a minor character during the 'Deception' events. Say, a civilian on Coruscant who witnesses some of the events unfold but misinterprets them. This could lead to a whole chain of events where their false assumptions create new problems or solutions in the Star Wars universe. Also, a plot could revolve around a Sith trying to use the deception for their own gain, but getting caught in a web of their own making.
One interesting plot idea could be Revan emerging from the past and influencing the events of the Clone Wars in unexpected ways. For example, he might have knowledge of a hidden Sith plot that could change the course of the war. Another could be Revan training a new group of Jedi or even influencing Anakin Skywalker's path, perhaps trying to prevent his fall to the Dark Side.
One plot idea could be exploring her relationship with her clone troopers in more depth. Maybe there's a mission where they have to rely on each other in an unexpected way. Another could be a story about her training a young Jedi padawan during the Clone Wars, showing her teaching methods and how she imparts the Jedi values.
One idea could be a story where a new, young Jedi discovers a hidden Sith artifact that has the power to control the Force in ways not seen before. This could lead to a race between the Resistance and the First Order to either obtain or destroy it.
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.