The plot could involve the 501st discovering a conspiracy behind Order 66. They might start to question why they are being ordered to kill the Jedi, who have been their comrades in arms. They could find evidence that the Sith are manipulating the situation for their own gain, and thus choose to disobey the order to prevent the destruction of the Jedi Order and the imbalance it would cause in the galaxy.
A clone trooper from the 501st could be a main character. Maybe a sergeant who has a strong sense of justice and starts to question the orders they receive. He could be the one to rally his fellow clones to disobey Order 66.
The plot might involve a clone who has a unique experience that makes him realize the wrongness of Order 66. For example, he could have been saved by a Jedi in the past. This clone then convinces other clones around him to disobey. They might join forces with some remaining Jedi and form a resistance against the new regime that's trying to take over after the purge of the Jedi. It could be a story full of action, as they fight against the forces that still support the execution of Order 66.
A clone medic could be a main character. He has spent a lot of time treating both clones and Jedi, and he realizes that the Jedi are not the enemies they are made out to be in the lead - up to Order 66. Alongside him could be a female Jedi knight who is a skilled fighter and diplomat. She uses her skills to try and persuade other clones to disobey the order. And perhaps there's a clone who was experimented on and has enhanced abilities, and he becomes a crucial part of their resistance against Order 66.
One possible scenario could be that a group of clones have formed strong bonds with the Jedi they serve. They might see through the sudden and unethical nature of Order 66. For example, a clone who has fought side by side with a Jedi for years realizes that the Jedi has always been honorable and just, and decides to disobey the order. Another scenario could be that there is a malfunction in the clone's inhibitor chip, causing them to resist the order. In some fanfictions, clones may also receive a counter - order from a different source that makes them question and ultimately disobey Order 66.
Captain Rex is often a likely candidate in fanfiction. He has a very close relationship with Ahsoka Tano and has seen the good in the Jedi through her. His loyalty to her might make him more likely to disobey. Another could be Commander Cody, if in a different scenario where he has more time to think about the implications of the order rather than blindly following it. He has worked closely with Obi - Wan Kenobi and might come to realize that the order is wrong.
Perhaps it's about their first time sharing a meal. Tarzan shows Jane how he gathers food in the jungle, and they sit down to eat together. As they eat, they start to learn more about each other's worlds. Tarzan is amazed by Jane's proper table manners, and Jane is intrigued by Tarzan's natural and raw way of eating.
The plot could involve Hermione trying to reform the St Trinians' school. She sees all the chaos and unruliness there and decides to use her Gryffindor courage and Ravenclaw intelligence to bring some order. Along the way, she has to deal with the unique personalities of the St Trinians girls, who are not used to the strict Hogwarts - like discipline she tries to introduce.
It could involve time travel. Maybe a character from 'the order' travels to the future and has to adapt to new magical or technological advancements there. They might encounter new forms of magic or face challenges that the future presents.
It could be that a member of the Order, out of jealousy or a wrong perception of Hermione's power, convinces the others that she is a liability. So, they betray her by not believing in her when she discovers something important or by preventing her from using her skills to help. Hermione, being the strong - willed character she is, would then strive to prove them wrong and expose the real issues within the Order.
Well, perhaps the members of the order find themselves in a future where their magic has evolved in unexpected ways. They might encounter new enemies or challenges that are based on futuristic technology that they have to adapt to using their magical skills.