Maybe there's a plot where Harry discovers a connection between the Force in the Star Wars world and magic from his own world. So, he tries to teach some of the more receptive clone troopers basic magic spells, which in turn gives them an edge in combat against the Separatist droids. This could lead to a whole new dynamic within the clone army.
One interesting plotline could be the clone trooper's struggle with his pre - determined identity. Since clone troopers are created for a specific purpose, the protagonist might question his loyalty and find new meaning in life. Another could be his interactions with well - known Star Wars characters, like Jedi, and how he influences the events of the Star Wars universe from a different perspective.
There are fanfictions that focus on the individual experiences of clone troopers. For example, a story might follow a clone trooper who gets separated from his unit during a battle. He has to survive on his own in a hostile environment, all while dealing with his own identity as a clone. Some fanfictions also explore the relationships between clone troopers and their Jedi generals in more depth, like how they communicate and trust each other on and off the battlefield.
One possible plot could be that a Clone Trooper somehow gets transported to the Harry Potter universe. Maybe through a magical experiment gone wrong. He then has to adapt to this new world of magic while still having his combat skills from being a trooper. He could end up teaching the Hogwarts students some self - defense techniques that are more physical in nature compared to magic.
Well, obviously Harry is one of the main characters. He brings his own set of skills, personality, and backstory from the Harry Potter universe. The clone troopers are also main characters. They can be individual clones with distinct personalities, like Rex or Cody. There might also be some Jedi characters who cross paths with Harry and the clones, as the Jedi play a significant role in the Star Wars universe and would likely be involved in any major events.
There are many Clone Trooper OC fanfictions where the OC is a medic. In these stories, the OC might have to deal with not only the physical wounds of the Clone Troopers but also their mental and emotional stress. It shows a different side of the Clone Wars, focusing on the care and support within the troops.
One idea could be a crossover with the Star Wars Rebels universe. Clone troopers could interact with the Ghost crew, leading to some interesting battles and alliances. For example, a group of clone troopers who survived Order 66 could join forces with the rebels to fight against the Empire.
Perhaps Naruto is transported to the clone trooper universe. He might initially be confused but then decides to help the clone troopers in their fight against the Separatists. He could use his shadow clone jutsu to create a large number of clones and turn the tide of battles, much to the amazement of the clone troopers and their commanders.
In this fanfic, Jaina could have a plotline where she has to train a group of younglings during the Clone Wars. This would be challenging as she not only has to protect them from the physical dangers of the war but also from the influence of the Dark Side. She might face situations where the younglings are in danger of being kidnapped by the Separatists or influenced by a Sith agent. Jaina would then have to use her own unique teaching methods and her connection to the Force to keep them safe and on the path of the Light Side.
Well, a really cool plot twist could be that the reincarnated clone trooper finds out that they were actually created with a secret purpose. Maybe they were designed to be a sleeper agent for the Sith all along, but their newfound consciousness rebels against this. Or perhaps they discover that they are a clone of a clone, which gives them some sort of unique genetic quirk that makes them immune to a certain type of weapon. Also, they could find out that their 'reincarnation' was actually part of a Jedi experiment gone wrong, and now they have to deal with the consequences while still fighting in the war.
Maybe Harry Potter could be magically transported to the Star Wars universe and become a Clone Trooper. He might use his magic skills to help the Clone Troopers in their battles, like using spells to deflect blaster fire or heal wounded troopers.