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.
Maybe a Clone Wars era weapon or technology is rediscovered during the Rebels time. The Rebels could struggle to understand it at first, but with the help of some old Clone Wars data logs, they manage to unlock its power. This could turn the tide in a major battle against the Empire. It would be interesting to see how the different aesthetics and combat styles of the two eras blend together in the fanfiction.
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.
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 a crossover with the original Star Wars trilogy characters. For example, having Luke Skywalker meet the Rebels crew and learn from their guerilla warfare tactics against the Empire. It would be exciting to see how their different fighting styles blend and how they interact with each other.
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 there could be a lost Mandalorian artifact that the Rebels accidentally discover. This draws the attention of a group of Mandalorians who think the Rebels are trying to steal it. As a result, they have to work together to figure out the true purpose of the artifact and face off against a common enemy who also wants it for their own evil plans.
There are several great plot ideas. For instance, imagine a situation where Yoda, before his death, set in motion a series of events that are only starting to unfold during the Rebels' time. Maybe he planted the seeds for a new Jedi order in a very secretive way. A young Rebel might stumble upon these secrets. Another idea is that Yoda's teachings, which were thought to be lost, are rediscovered by the Rebels through an ancient Jedi artifact. This discovery changes the way they approach the fight against the Empire. And what about a story where Yoda's influence reaches out to a non - Force - sensitive character in Rebels, inspiring them to do great things for the Rebellion in a different way?
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 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.