One idea could be a fanfic where the Captain Earth characters have to face an alternate dimension version of themselves. It would be a great way to explore different character traits and how they interact with their own doppelgangers.
One idea could be a time - travel fanfic where Captain Marvel and Captain America team up in a different era. Maybe they end up in the 1920s and have to deal with a Hydra - like threat that's starting to form early. Another could be a fanfic where they swap powers for a day and have to learn to adapt to each other's abilities. For example, Captain America trying to control Captain Marvel's photon blasts and Captain Marvel having to rely on just her combat skills like Cap usually does.
You could write an 'After Earth' fanfic that takes place in a different part of the planet that we didn't see in the movie. It could be a frozen tundra area where the characters have to adapt to extreme cold and find new ways to survive. They might discover ancient artifacts buried in the ice that hold the key to a better future for all the people on After Earth.
Well, you could write a 'Captain America experiment fanfic' where the experiment was part of a larger, inter - dimensional experiment. Maybe in this fanfic, Captain America's experiment not only changed him physically but also opened a portal to another dimension. And from that dimension, new threats or allies come into play. You could also have a story where the experiment was a test by an ancient civilization that was long forgotten, and as Captain America discovers the truth about the experiment, he has to deal with the implications of this ancient knowledge.
One idea could be Naruto arriving on Earth during a major global crisis, like a widespread natural disaster. He could use his ninja skills to rescue people. For example, his shadow clone jutsu would be very useful in searching for survivors in multiple locations at once.
You could also focus on the villains in this AU. How do they take advantage of the separation? Maybe they try to keep the characters apart permanently to gain more power in the city. You can show their devious plans and how the heroes have to overcome them in this new, separated world.
One idea could be exploring the perspectives of the minor characters during the conflict. For example, how an ordinary citizen in Sokovia feels about the heroes' actions. Another could be a what - if scenario where Steve Rogers and Tony Stark managed to resolve their differences before the big fight. Maybe a story about a new superhero who emerges during the civil war and tries to mediate between the two factions.
A plot could be about an alternate universe where Captain Marvel is initially distrusted by the Avengers. She has to prove herself and in the process, they all learn more about each other's powers and pasts. This could lead to some great character development and new alliances within the team.
One idea could be about a human who has to form an alliance with different monster girl tribes to save the Earth from a common threat, like an ancient evil that has been awakened. This would involve a lot of character development as the human learns about each monster girl's culture and abilities.
One idea could be a time - traveling adventure where the Doctor and Captain Jack team up to stop an alien threat that is disrupting the space - time continuum. They could visit different historical periods and use their unique skills to outwit the enemy.
Perhaps the ANBU captain is tasked with training a new group of recruits. It could show his strict but fair teaching methods and how the recruits grow under his guidance. This could involve various training arcs and character development for both the captain and the recruits.