One idea could be a mercenary who is hired by a mysterious Sith Lord to steal a powerful Jedi artifact. The mercenary then has to navigate through various planets, dealing with both Jedi and Sith along the way.
Maybe a group of mercenaries form an alliance to protect a small, neutral planet from being invaded by the Empire. They have to use their diverse skills and resources to fend off the Imperial forces. This could involve epic space battles and ground combat.
A mercenary could start off working for the wrong side, say the Hutts. But then they have a change of heart when they see the atrocities committed by the Hutts against innocent people. So they switch sides and help the Rebel Alliance, all while trying to redeem themselves in the eyes of the galaxy.
A great plot idea is that the fem OC mercenary discovers a hidden map to a long - lost Jedi temple. However, she has to outwit a group of Sith cultists who also want the map. As she travels across different planets in search of the temple, she teams up with a local resistance group. Along the way, she uncovers secrets about her own past that are linked to the Jedi. This would make for an exciting and complex fanfiction plot.
A common plot idea is the mercenary getting caught in the middle of a galactic power struggle. For example, between the Empire and the Rebellion. They might be hired by one side, but then realize they've been used or that the other side has a more just cause. Another idea is a quest for a valuable artifact. The mercenary could be hired to retrieve it, but face many obstacles and other parties also after it. Or, they could be on a personal vendetta against a powerful crime lord in the Star Wars universe.
One idea could be exploring the origin of a new, mysterious force - user in the Shadow Wars. Maybe it's a forgotten Jedi or Sith technique that resurfaces and causes chaos. Another could be focusing on the relationship between a group of rebels and how they deal with the added threat of the Shadow Wars.
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.
One idea could be exploring the backstory of the apprentice before they met their master. Maybe they had a family on a far - off planet that was destroyed, which led them to seek power. Another could be a story where the apprentice has to choose between loyalty to their master and doing what they believe is right. For example, if their master orders them to destroy an innocent village, they might rebel.
One idea could be that the triplets are force - sensitive and are secretly trained by an old Jedi master in hiding. They grow up to be a powerful force against the dark side.
One idea could be a story where a god - like being from another dimension enters the Star Wars universe and has to choose a side in the galactic conflict. Maybe this being has the power to manipulate the Force in ways no Jedi or Sith has ever seen before.
One idea could be a story where a young Jedi discovers the Darksaber and has to resist its dark influence. Maybe they are on a mission to return it to its rightful place.
A fanfiction could explore what would happen if the Jedi had to face the power of the One Ring. The Jedi's connection to the Force might give them some resistance to the Ring's corrupting influence, but it would still be a great struggle. It could also involve characters from both universes learning from each other's cultures and ways of combat.
A cool plot idea could be that the Transformers are mistaken for a new type of Sith - created abomination. The Jedi initially try to destroy them, but then realize they are something different. Another idea is that a Transformer becomes a Jedi Knight, using its unique abilities in combat and its own code of honor which is similar to the Jedi Code.