A plot could involve Anakin and Ahsoka being framed for a crime within the Jedi Order. They then have to work together to clear their names, all while uncovering a conspiracy within the Order that could have far - reaching consequences for the galaxy.
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.
In many fanfictions, Ahsoka and Anakin's relationship is complex. Anakin was Ahsoka's master during the Clone Wars. Their bond was like that of a brother and sister at times. Ahsoka learned a great deal from Anakin, not just about the Force but also about combat and decision - making. Anakin, on the other hand, saw Ahsoka as someone he could trust and rely on in the chaos of war.
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.
One idea could be exploring a mission that Ahsoka and Anakin go on where they get stranded on an unknown planet. They have to rely on each other's skills to survive and in the process, Anakin imparts some deeper Jedi wisdom to Ahsoka. Another could be a story set during the Clone Wars where they face a new and powerful Sith enemy together, forcing them to combine their fighting styles in a unique way.
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.
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.
Anakin and Padme could go on a secret mission together during the Clone Wars. They'd have to hide their relationship while facing all kinds of dangerous enemies and situations. It would be exciting to see how they use their respective skills, Anakin's Jedi powers and Padme's political acumen, to get out of trouble.
A more complex plot could be Anakin's encounter with a Sith artifact during the Clone Wars. He's tempted by its power, and it starts to influence his actions and thoughts. He has to struggle with this newfound temptation while still fighting in the war, which could foreshadow his fall to the dark side.
In some fanfictions, Anakin's past as a slave greatly influences his character during The Clone Wars. It might be explored how his experiences of being a slave shape his views on freedom and power. For example, he could be more empathetic towards the enslaved in certain storylines, or his fear of losing his new - found freedom could drive some of his actions during battles and political situations in the Clone Wars era.
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.