A really cool plot idea could be that the clones team up with the villains from the Naruto universe. They do this because they feel betrayed by Naruto or the Hidden Leaf Village. This would lead to some epic battles where Naruto has to face his own clones and the villains at the same time. There could be a lot of emotional turmoil as Naruto tries to understand why his clones turned against him and if there's a way to bring them back to his side.
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.
Perhaps a romance between a ninja from a different village and a Naruto clone. They meet during a battle in the Clone Wars and initially see each other as enemies. But as they interact more, they start to have feelings for each other. They then have to face the challenges of being from opposing sides while also dealing with the chaos of the war.
One plot idea could be that Naruto, being his energetic self from the Naruto universe, gets teleported to the Clone Wars universe. There, he starts to form relationships with various female characters, like Ahsoka Tano. Maybe he uses his ninja skills to help in the Clone Wars, and as he does, he catches the attention of other female clones or Jedi, gradually building a harem around him. Another idea is that a Sith Lord notices Naruto's unique chakra and tries to use him to create a powerful army, but the female characters team up with Naruto to stop it, leading to deeper emotional bonds.
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.
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.
Perhaps a fanfiction where some of the Naruto characters are actually clones themselves, like in The Clone Wars. Naruto could be a special clone created with a combination of chakra and the Force. His purpose could be to bring peace between the two universes. Hinata could be a healer in this new world, using her gentle nature and Byakugan to sense injuries and use the Force to heal them. This would mix the two universes in a unique way and create a lot of new storylines.
One idea could be that Naruto is somehow transported to the Star Wars universe during the Clone Wars. He could use his ninja skills, like his shadow clone jutsu, in unique ways on the battlefields. For example, his clones could be used to create diversions while the Jedi try to outmaneuver the Separatist droids.
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 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.