One interesting storyline could be a young Superman and Batman teaming up for the first time in a kid - friendly adventure. Maybe they are trying to stop a group of small - time villains who are stealing toys from all the kids in Gotham. They use their unique powers and detective skills respectively to track down the bad guys and return the toys.
Another possible storyline is that Superman and Batman are turned into kids themselves in a magical mishap. They have to rely on their child versions of themselves to figure out how to reverse the spell. Along the way, they learn a lot about what it's like to be a normal kid while still having their heroic instincts, which makes for a fun and educational story for the readers.
A cool story could be about them having a friendly competition to see who can solve a series of mysterious crimes in the other's city first. Along the way, they learn more about each other's methods and develop a deeper respect for one another. This also gives an opportunity to explore the different atmospheres and challenges of Gotham and Metropolis.
One interesting storyline could be a redemption arc for Superman. In the Injustice universe, Superman has gone down a dark path. A fanfiction might explore how Batman tries to bring back the good in him, with lots of emotional confrontations and moral debates between the two.
One possible storyline could be that Batman has to use his detective skills to find out a hidden threat to Superman before saving him. Maybe there's a kryptonite - based weapon that only Batman can detect and disable.
One interesting storyline could be their child having to hide their powers in a normal school. They'd struggle to fit in while also having the responsibility of their superhero heritage. Another could be the child getting kidnapped by a villain who wants to use their unique genetic makeup for evil.
A really interesting plot could be that the child is kidnapped by an old enemy of either Wonder Woman or Batman. The kidnapper wants to use the child to get revenge on the heroes. The child then has to use their wits and the powers they've inherited to escape. Along the way, they might make new friends or discover secrets about their parents' pasts that help them in their journey.
One interesting storyline could be a reimagining of Batman's first encounter with the Joker in the 1939 fanfiction context. Maybe the Joker starts as a small - time criminal and Batman has to figure out his true motives early on.
One interesting storyline could be Supergirl and Superman teaming up to face a powerful new villain from another dimension. They would have to combine their powers and learn to work in perfect sync to defeat this threat.
Maybe a storyline where Mala has some unique powers that Superman doesn't have, and they have to team up to face a powerful enemy. Their combined efforts would make for an exciting adventure, with each using their own strengths to overcome obstacles.
One interesting storyline could be where Superman and X - 23 team up to fight a common enemy like Darkseid or some other powerful villain. X - 23's combat skills and Superman's superpowers would make for an exciting combination in battle.
A very common plot in such fanfiction is the origin story of their brotherhood. It could involve some secret history of their families or a hidden prophecy. Also, there are storylines where they have a falling - out as brothers, maybe because of a misunderstanding about their powers or their roles. But then they reconcile and become stronger together. There are also stories where they discover new powers or abilities because of their brotherly connection.