The storyline could focus on Batman forming his own team. He might gather some of his old allies or even some new characters. This new team could operate in Gotham and deal with threats that the Justice League might overlook.
After Batman leaves in the fanfic, the Justice League might struggle without his strategic mind. They could face a series of defeats that make them realize how important he was. This could lead to them trying to win him back. Meanwhile, Batman is off on his own adventures, facing new villains that are unique to his new solo path.
Another possibility in the fanfic is that Batman discovers some dark secrets within the Justice League. Maybe there's something corrupt or dangerous about the way they operate that he can't tolerate. So, to protect his own integrity and the safety of Gotham, he chooses to leave the team.
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.
Wonder Woman would probably respect Batman's decision. However, she would also be concerned about the void his departure would leave in the team. She might start taking on more of a leadership role to fill the gap, while also hoping that Batman would return one day.
The story could develop in a way that Harry goes through a period of self - discovery. Without the Gryffindor identity, he has to re - evaluate who he is. He might explore different kinds of magic that Gryffindor house never encouraged. This exploration could lead him to new powers and a new understanding of the wizarding world.
In some cases, the story might focus on Hermione's journey after leaving. She could end up in a new and strange part of the wizarding world, meet different characters, and learn new magic. Meanwhile, Harry might be on a quest to find her and in the process, uncover secrets about the wizarding world that they never knew before. This can lead to a reunion later on, but with both of them changed by their experiences.
Naruto himself might start to form his own group or alliance outside of Konoha. He could gather other outcasts or those who have a grudge against the major ninja villages. This new group could then have its own goals, like trying to reform the ninja world in a way that is different from how Konoha and the other villages operate. As the story progresses, there would be inevitable clashes between Naruto's new group and Konoha.
The story could develop with Issei forming his own group. He might gather other characters who also feel left out or have similar goals. This new group could then become a rival to Rias' peerage, leading to interesting battles and power plays.
Natasha's own journey might be explored. She could start working with a new group or go on a personal quest for redemption. Maybe she teams up with some old acquaintances from her past in the Red Room to take down a common enemy.
In a fanfic where Batman is injured, it could lead to many interesting plot developments. Maybe the other Justice League members have to step up their game. Superman might take on a more protective role over Gotham in Batman's absence. Wonder Woman could be the one to lead the investigations that Batman usually handles. This kind of injury to Batman can create a shift in the power dynamics within the Justice League.
I really like 'Batman: Shadows in the League'. In this fanfic, Batman has to deal with a secret threat that is undermining the Justice League from within. It shows his detective skills as he uncovers the mystery. The characterizations are on point, especially how Batman interacts with Superman in a more tense situation than usual.