One plot idea could be Ahsoka getting lost in a strange, uncharted part of the galaxy during the Clone Wars and having to rely on her wits and the help of some unexpected allies to find her way back. Another could be Ahsoka facing a dark side version of herself, created by a Sith's manipulation of the Force.
One plot idea could be Ahsoka and Lux teaming up to uncover a hidden Sith plot within the Clone Wars. They might stumble upon a secret Sith artifact that the Separatists are trying to use to gain an upper hand.
Maybe a story where Ahsoka has a premonition about Anakin's fall to the dark side. She tries to prevent it in secret, which leads to all sorts of dangerous situations and moral dilemmas as she struggles with whether to tell the Jedi Council or handle it on her own.
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.
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 idea could be a crossover where RWBY characters are somehow transported to the Clone Wars universe. They could team up with the Jedi or Clone Troopers to fight a common enemy, like a new type of Grimm that has invaded the Star Wars galaxy.
Maybe in the fanfiction, the clones start to gain special powers different from Naruto. For example, some clones could have the ability to control time on a small scale. This would create a whole new dynamic in the battles and the overall story.
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.