For a Star Wars Clone Wars crossover fanfiction, you could explore the idea of a group of Mandalorians from different time periods coming together during the Clone Wars. They might have different views on the war and the Jedi. Some could be more traditional, while others might be influenced by the changing politics of the galaxy. Their presence could add a new layer of conflict and intrigue. They could interact with Clone Troopers, Jedi, and even the Sith in unexpected ways, leading to some epic battles and character - development moments.
One idea could be to cross it with another sci - fi universe like Star Trek. Imagine the Jedi and the Federation crew working together. Another could be a crossover with the Transformers universe, where the clones team up with the Autobots to fight a common enemy. Maybe also a crossover with the Mass Effect universe, with the clones and Shepard's crew sharing combat strategies.
One plot idea could be that a character from Clone Wars gets accidentally sent to the time period of Rebels. For example, Ahsoka Tano could end up in the middle of a battle between the Rebels and the Empire. She might use her knowledge from the Clone Wars era to help the Rebels in unexpected ways, like teaching them some old Jedi combat techniques that were lost over time.
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.
Perhaps a fanfiction where a group of gamers create their own custom clone units in the game and then those units somehow become real in the Star Wars universe. They then have to train and lead these unique clones in battles.
One plot idea could be exploring her relationship with her clone troopers in more depth. Maybe there's a mission where they have to rely on each other in an unexpected way. Another could be a story about her training a young Jedi padawan during the Clone Wars, showing her teaching methods and how she imparts the Jedi values.
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 idea could be a story about a Clone Trooper who is wrongly imprisoned by the Separatists. He then has to use his combat skills and wits to escape and bring back crucial information to the Republic. It could show his internal struggle as he faces the harsh conditions of the prison.
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.