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.
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.
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 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.
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.