Many 'clone troopers order 66 fanfic' delve deep into the moral conundrum of the clone troopers. The clones are essentially slaves to their programming. When Order 66 is issued, they are forced to choose between their ingrained sense of duty and their sense of right and wrong. Some fanfics might show clones who are able to override their programming due to their strong moral compass developed through their interactions with the Jedi. Others might show the tragic consequences of clones who blindly follow the order, despite their inner doubts, leading to a downward spiral of guilt and self - loathing.
In some 'clone troopers order 66 fanfic', it focuses on the aftermath of Order 66 from the clone troopers' perspective. Some clones might feel a deep sense of guilt for what they've done. A story could revolve around a clone who is haunted by the memories of killing a Jedi he respected. He then tries to atone for his actions, perhaps by helping any remaining Jedi or trying to expose the true nature of the Sith's plot that led to Order 66.
The main difference is their origin. Clone Troopers were cloned from Jango Fett, so they had a genetic basis for their skills. Storm Troopers were recruited from various sources. In fanfic, this can lead to differences in how they are portrayed in combat, with Clone Troopers having more in - built combat instincts.
Clone Troopers would probably win. They were bred for combat, had better training initially, and a higher level of genetic customization which could give them an edge in combat compared to Storm Troopers, who are often depicted as less accurate and more bumbling in the movies.
The story of how clone troopers were created is fascinating. They were made from the genetic template of Jango Fett. This process led to an army that was initially very uniform in appearance and abilities. However, as they faced different battles, they started to form their own personalities. Some became more strategic, while others were known for their brute strength in combat.
Earth would likely have a mixed reaction. The scientific community would be fascinated by the Clone Troopers' genetic makeup and advanced weaponry. Civilians might be scared, thinking it's an alien invasion. However, some groups, like military enthusiasts, could see them as allies and want to cooperate. There would also be a lot of speculation about their purpose and where they came from. If the Clone Troopers came in peace, there could be a slow process of integration and cultural exchange.
The novel you mentioned might be the book, What to Do If You're Taken by the Missy. The male protagonist, Fang Ye, accidentally became attached to the Missy, Han Niannian, because he was kidnapped. The girl who was later adopted by the assistant should be Han Niannian. I hope you like my recommendation. Muah ~
The Clone Wars comics usually have a chronological order based on the events in the Star Wars universe. You can start with the earliest published issues and follow the series as they were released.