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.
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 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 could involve Jesse and Kix being sent on a secret mission. They discover a conspiracy within the clone army that could have far - reaching consequences. As they dig deeper, they face challenges like distrust from their own comrades and attempts on their lives. They must use their wits and combat abilities to expose the truth.
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.
Another interesting angle would be to have a Clone Wars character, like Anakin Skywalker, land on Earth for some reason. His presence could cause a stir among the people, and his Jedi powers would be both fascinating and potentially terrifying to the Earth population.
One idea could be exploring the lives of clone troopers who start to question their loyalty to the Republic. They might discover some dark secrets about the Jedi or the Senate that make them consider joining a rebellion. Another plot could involve a young padawan who teams up with a group of clones to fight against a new Sith threat that the Jedi Council is unaware of. Maybe a group of clones find an ancient force - related artifact that gives them unique powers and they use it to fight for their own freedom.
One idea could be exploring the backstories of the clone troopers in more depth. Maybe focus on a particular clone and his journey of self - discovery during the war. Another could be creating a new character, a young Jedi padawan who gets caught up in a mission that wasn't supposed to be for them but ends up playing a crucial role.
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.
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.