One interesting plotline could be the 501st's special missions that are not shown in the main Clone Wars series. For example, they might be sent on a covert operation to rescue a group of Jedi who are trapped on a Separatist - held planet. This would involve a lot of strategic planning and intense combat situations.
A third plotline could be about the 501st's encounter with a new and powerful enemy. This enemy could have unique abilities or technology that the 501st has to figure out how to counter. It would put their training and adaptability to the test and lead to some exciting battles.
Another plotline could focus on the individual relationships within the 501st. Maybe there's a story about two clone troopers who have a strong friendship and how they support each other through the hardships of war. It could show their different personalities and how they grow together as soldiers.
One interesting plotline could be the complex relationships between the clone troopers and the multiple characters in the harem. For example, how they navigate loyalty to the Republic while dealing with their personal feelings for different individuals. Another could be a story where a character from the Clone Wars has to protect the members of the harem during a dangerous mission, leading to character development and deeper emotional bonds.
One interesting plotline could be the rookies facing an unexpected and powerful Sith enemy. Maybe they have to use their basic training in creative ways to survive.
One unique plotline could be a time - travel story. A character goes back in time to the start of the Clone Wars and tries to prevent certain events from happening. Another could be a story where the clones develop their own culture and start to question their purpose. And there's also the plotline where a Jedi falls in love with a Separatist, creating a conflict of loyalty.
One interesting plotline could be Luke Skywalker being mysteriously transported back in time to the Clone Wars era. He could then use his Jedi skills, which he learned in his own time, to influence the battles in unexpected ways. For example, he might teach some Clone Troopers unique combat techniques.
A common plotline is Rex's relationship with Ahsoka. Some fanfictions explore how they grow closer as comrades during the Clone Wars. For example, one might show Rex being there for Ahsoka during a particularly tough mission, and how their bond deepens because of it.
A plotline could be a droid uprising within the droid army. The droids could start to rebel against their Separatist masters. This could be due to a glitch in their programming or because they've been exposed to new ideas. They might then form their own society and try to co - exist with the other species in the Star Wars universe.
One interesting plotline is the complex relationships among the clones. They start to question their purpose and identity, which adds a deep layer of moral and ethical exploration.
One interesting fanfiction could be about the 501st's adventures in uncharted planets during the Clone Wars. They might encounter strange alien species and have to use their combat skills and teamwork to survive.
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.
One possible plotline could be Luke's discovery of a long - lost Jedi technique during the Clone Wars. Maybe he uncovers it while on a mission to rescue some clones. Another could be his interaction with famous Clone Wars era characters like Anakin or Obi - Wan. He might learn valuable lessons from them that shape his future as a Jedi.