The Grand Inquisitor could be on a mission to study the Jedi during the Clone Wars for future reference in hunting them down. He might infiltrate the Jedi Order undercover, observing their training methods, their weaknesses, and how they interact with the clones. This would give him valuable insights that he could use in his later role as an Inquisitor, but he also has to be careful not to be discovered by the Jedi during this time.
The Grand Inquisitor might interact with Anakin Skywalker. This would be really interesting as Anakin is on the verge of turning to the dark side during the Clone Wars. The Inquisitor could try to nudge Anakin further towards the dark side, or Anakin could sense the dark presence in the Inquisitor and be suspicious of him.
One possible motive could be to gain more power. In the Clone Wars era, there are many opportunities for someone with his skills to manipulate the situation. He could try to amass power by influencing key players on both sides of the war. Another motive might be to study the Jedi at their peak. He was created to hunt them later, so understanding their ways during the Clone Wars could give him an edge in the future.
If the Grand Inquisitor travels to the Clone Wars era, things would be very different for him. First of all, the technology and the state of the galaxy are different. The Jedi are more respected and in a position of power. He would probably be seen as an oddity or a threat right away. His presence could disrupt the balance of power between the Jedi and the Sith in that era. He might try to use the Separatist movement to his advantage, maybe by influencing some of the leaders to target Jedi specifically. But the Jedi would be on high alert, and his every move would be closely watched.
One interesting plot idea could be exploring Dooku's early days in the Sith. Maybe showing how he was gradually corrupted by Sidious. Another could be a story where Dooku has a change of heart briefly and tries to make amends in some small way during the Clone Wars, but is quickly pulled back into the dark side by Sidious' influence. A third idea could be a fanfic that focuses on Dooku's relationship with his former Jedi colleagues during the Clone Wars, like how he feels when facing them in battle.
One idea could be focusing on a young clone trooper who discovers he has unique Force abilities. He then has to hide this from his superiors while trying to figure out what it means.
One idea could be exploring the backstories of the clone troopers in more detail. Maybe focus on a particular clone and his relationships with his brothers. Another could be creating a new adventure for Anakin Skywalker during the Clone Wars that wasn't shown in the original series. For example, he could be sent on a secret mission to a planet that has a powerful and ancient Sith artifact.
In a 'harry becomes inquisitor' fanfic, Harry could be appointed as inquisitor after some mysterious events in Hogwarts. He uses his unique perspective, having faced so many challenges as a student, to make the inquisitorial system more empathetic. He might focus on helping students who are wrongly accused rather than just blindly punishing those suspected of rule - breaking. This would change the whole dynamic of the inquisitorial role in Hogwarts.
A plot could involve Jesse and Kix being sent on a secret mission. They discover a conspiracy within the clone army that could have far - reaching consequences. As they dig deeper, they face challenges like distrust from their own comrades and attempts on their lives. They must use their wits and combat abilities to expose the truth.
One idea could be exploring the lives of clone troopers who start to question their loyalty to the Republic. They might discover some dark secrets about the Jedi or the Senate that make them consider joining a rebellion. Another plot could involve a young padawan who teams up with a group of clones to fight against a new Sith threat that the Jedi Council is unaware of. Maybe a group of clones find an ancient force - related artifact that gives them unique powers and they use it to fight for their own freedom.
Well, you could have a fanfic where Darth Vader travels back in time to the Clone Wars era. He could try to change certain events to better suit his later goals as a Sith. For example, he might attempt to influence the development of the clone army in a way that would make them more loyal to him personally rather than the Jedi or the Republic. This could lead to all sorts of conflicts and power struggles within the already complex Clone Wars setting.