One plot idea could be exploring her relationship with her clone troopers in more depth. Maybe there's a mission where they have to rely on each other in an unexpected way. Another could be a story about her training a young Jedi padawan during the Clone Wars, showing her teaching methods and how she imparts the Jedi values.
Clone Commander Bly could also be paired with her. Since he serves under her, there could be stories about their mutual respect and how they work together in battle. Maybe a story where Bly saves her life in a crucial moment, deepening their bond.
Well, it could be about Naruto being transported to the Clone Wars universe and teaming up with Aayla Secura. Maybe they fight against common enemies using Naruto's unique jutsu and Aayla's Jedi skills.
Another idea is that there is a common enemy that threatens both Naruto's world and the Clone Wars universe. Naruto and Aayla Secura have to gather allies from both worlds. Naruto would call upon his friends like Sasuke and Sakura, while Aayla would get help from the Jedi Council. They would then combine their different fighting styles and powers to defeat this powerful enemy.
At first, there might be some misunderstandings. Naruto's boisterous nature could seem strange to Aayla, and her use of the Force might seem like magic to Naruto. But as they spend more time together, they would start to bond. They could train together, with Naruto showing Aayla some of his ninja training techniques and Aayla teaching Naruto about lightsaber combat and the ways of the Force. Their relationship could grow from mutual curiosity to a strong friendship or even more, depending on how the fanfiction is written.
Naruto would probably be really curious about the Jedi culture. He might be fascinated by the concept of the Force, which is somewhat similar to chakra in his world. He would likely ask a lot of questions to Aayla Secura about how the Jedi train and use their powers. He could also try to learn some Jedi techniques, like lightsaber combat, but with his own Naruto - style twist.
One possible fem clone OC could be a highly skilled sniper. In fanfiction, she might have unique markings on her armor that distinguish her from the male clones. She could befriend some of the Jedi, like Ahsoka Tano, and together they face various challenges during the Clone Wars.
One interesting clone fanfiction could be about a clone's journey of self - discovery outside of his military duties. For example, a clone might start to question the purpose of the war and his place in the galaxy.
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.
You can start by looking on fanfiction websites such as Archive of Our Own (AO3). It has a large collection of fan - created works, including many for 'Star Wars: The Clone Wars' and specifically about the clones.