One possible storyline could be that Batman is exposed to a mind - controlling substance. This makes him turn against his allies in Gotham. He might start using his advanced technology and combat skills to take over the criminal underworld instead of fighting it.
A storyline could involve Nightwing being framed for a crime in Gotham. Batman, believing the evidence at first, tries to bring him in. Nightwing, of course, resists as he is innocent, and this leads to their fight. As the story progresses, they both realize there's a bigger conspiracy at play.
One possible storyline could be that they are facing an extremely powerful and ancient evil. This evil has the power to corrupt the very essence of the world. Batman and Wonder Woman, in their attempt to stop it, find themselves in a situation where they have to sacrifice their lives. Maybe they are lured into a trap where the only way to prevent the evil from spreading across the universe is for them to use their combined powers in a self - destructive way.
In a fanfiction, it could be that a scientific experiment gone wrong in Gotham creates a mutant - like creature that has super strength and intelligence. This creature targets Batman as it sees him as a threat to its new - found power in the city. After a long and brutal battle, the creature overcomes Batman and kills him.
A possible storyline could be that Wonder Woman comes to Gotham to investigate some strange occurrences that seem related to her world. She teams up with Batman, and they discover a cult that is trying to summon an ancient evil. Along the way, they learn to respect each other's methods.
One possible storyline could be that Batman is on a mission in the Amazon and crosses paths with Hippolyta. They initially have a misunderstanding as Batman's methods seem strange to Hippolyta, but as they get to know each other, they find they have a mutual respect for justice. Batman learns about the Amazonian way of life and Hippolyta becomes intrigued by Batman's detective skills.
Another storyline might involve Batman leaving because of a personal crisis. For example, he discovers something dark about his past that makes him question his place in the Justice League. He might think that he's a liability to the team and decide to leave to protect them.
One possible storyline could be Harry growing up in Gotham, learning Batman's ways, and then suddenly discovering his wizarding heritage. He would have to adjust to the magical world while still holding onto his Batman - trained values. Another could be that Batman somehow ends up in the wizarding world and has a relationship there, resulting in Harry. Then the story could focus on how Harry uses his father's skills to combat dark magic.
One possible storyline could be that Batman discovers a conspiracy within the Justice League that endangers Gotham. So he and Robin decide to take on the League to stop it. Another could be that the Justice League is being mind - controlled, and Batman and Robin are the only ones who realize it and try to free their friends by fighting them. Or perhaps there's a misunderstanding where the Justice League believes Batman and Robin have turned bad, and they have to fight to prove their innocence.
One storyline could be that Jason discovers a plot against Batman early on. He then sets up a counter - plan and at the crucial moment, jumps in to save Batman from a deadly trap. This would show Jason's intelligence and his lingering care for Batman despite their past issues.
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.