One idea could be that a new villain emerges who has the ability to manipulate time, which affects both Young Justice's world and Central City where The Flash operates. The heroes from both groups have to work together to stop the villain before time is completely disrupted.
Definitely Kid Flash. He has a connection to both Young Justice and The Flash. His relationship with The Flash could be explored further, like how he feels about being in the shadow of the more famous speedster while also being a key member of Young Justice. And his powers could be a great asset in the crossover, as he can keep up with The Flash in terms of speed to a certain extent.
Barry Allen is a key member. He's the main Flash and often serves as a mentor figure. Wally West is also important. He has his own experiences and relationships within the team. Then there's Bart Allen, also known as Impulse. He brings a youthful and sometimes reckless energy to the Flash family's presence in the Young Justice universe.
The plot could revolve around a threat that only the Flash clone can stop. This would give the clone a chance to shine and prove its worth. It could also lead to a team - up with other Young Justice characters, like Robin or Aqualad. They might initially be skeptical of the clone but then come to rely on it as the story progresses.
The Flash clone in the fanfiction might have a different origin story compared to the original Flash. It could be the result of a scientific experiment gone wrong or a plot by a villain. This would add an element of mystery to the story.
Obviously, the Flash is one of the main characters. He brings his super - speed and unique personality to the story. And then, of course, members of the Justice League like Superman, Batman, Wonder Woman, etc. Superman with his super strength, Batman with his intelligence and gadgets, and Wonder Woman with her combat skills and Amazonian heritage are all likely to play important roles.
Another theme is the exploration of new powers and abilities. When they cross over into different universes or teams, characters often have to adapt to new powers or face enemies with unfamiliar abilities. It makes for some really interesting storylines. For instance, if a Young Justice character crosses over to a magical - based universe, they might have to figure out how to deal with magic for the first time.
One idea could be that Naruto is somehow transported to the Young Justice universe and his chakra is mistaken for a form of magic. This could lead to some interesting team - ups and misunderstandings as the Young Justice characters try to figure out who Naruto is and what his 'magic' can do.
A fanfiction about Naruto and Batgirl in the Young Justice setting could explore different themes. It could be about cultural exchange, as Naruto comes from a very different world than the DC universe. Their combined efforts could also be centered around protecting the innocent. Maybe they have to stop a powerful villain who is threatening both the ninja world Naruto comes from and the Young Justice world. Their different abilities would be crucial in this fight, with Naruto using his Rasengan and Batgirl using her Batarangs and martial arts skills.
There are many great authors out there. Some of the well - known ones are those who have been writing in the Young Justice fanfiction community for a long time. They often have a deep understanding of the characters, like Kid Flash. You can usually find them on popular fanfiction websites where their stories have high ratings and lots of reviews.