Nightwing is a great choice. He has a strong connection to Batman as his former sidekick. In an Injustice fanfiction, Nightwing could be the voice of reason when Batman starts to go too far in his fight against Superman. Their relationship, with all its history and baggage, can add a lot of depth to the story.
In the Injustice 2 Batman ending story, Batman manages to defeat Superman. He restores order to a world that has been torn apart by the chaos of the Injustice regime. With Superman out of the way, Batman is able to start rebuilding society, bringing back justice and the rule of law. He also has to deal with the remaining super - villains and ensure that they are locked away safely.
Batman himself is obviously very popular. He's the central figure and fans love to explore different aspects of his character in this 'injustice for all' scenario. His intelligence, combat skills, and unwavering sense of justice are always interesting to write about.
Perhaps a story where Batman discovers a conspiracy within the Injustice League that involves mind - controlling the heroes. It could delve into his detective skills as he tries to uncover the truth and save his comrades. This would be full of mystery and action.
One idea could be exploring Batman's internal struggle in the Injustice universe more deeply. Maybe he has a nightmare where he becomes like the tyrannical Superman, and this makes him question his own actions and methods even more.
Their relationship could develop through mutual respect. Batman respects Supergirl's power, and Supergirl respects Batman's intelligence and strategic skills. They start by working on small missions together and gradually build trust.
One idea could be that Batman tries to train Supergirl to better control her powers in the context of the Injustice 2 universe. He might see her as a potential force for good against the tyrannical regime. Another could be that Supergirl discovers a way to bring back the more heroic Superman she once knew, and Batman has to decide whether to trust her plan or not.
Obviously, Batman and Superman are the most prominent. Their complex relationship, which is a mix of friendship, rivalry, and ideological differences, makes them central to any fanfiction in this universe. However, characters like Wonder Woman also often play important roles. In some fanfictions, she may be caught in the middle of the Batman - Superman conflict, trying to mediate or having her own stance on the events that unfold.