Well, perhaps a plot where Wonder Woman is injured during a battle against the resistance led by Batman. Batman then has to take care of her and in the process, they start to have long conversations about their different views on justice. As she recovers, she begins to question her allegiance to Superman. This could lead to a split in the regime as Wonder Woman might start to work towards a more balanced form of justice, influenced by Batman's ideas.
One plot idea could be Batman trying to convince Wonder Woman to see the error of her ways in the Injustice universe. Maybe he shows her the long - term consequences of their actions on the common people. Another could be a story where Wonder Woman and Batman have to team up against a greater threat that makes them re - evaluate their stances in the Injustice conflict.
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.
One idea could be that Batman and Wonder Woman are both vying for the attention of a new superhero in town. Batman is jealous because Wonder Woman seems to have a natural connection with this new hero, perhaps due to their similar powers or backgrounds. Wonder Woman, on the other hand, is jealous of Batman's detective skills which the new hero seems to admire a great deal. This could lead to a series of challenges and competitions between Batman and Wonder Woman to prove who is more worthy of the new hero's friendship or alliance.
A possible plot could involve a mind - control situation. An evil sorcerer manages to put Robin under his spell and sends him to attack Batman and Wonder Woman. They are reluctant to fight Robin but have to find a way to break the spell without harming him. Meanwhile, they also need to stop the sorcerer from using Robin to carry out more devious plans, like stealing secrets from the Justice League.
One idea could be that a powerful new villain emerges who is a threat to both Gotham and Themyscira. Batman and Wonder Woman team up to track down the villain's lair. Batman uses his detective skills to analyze the clues while Wonder Woman uses her combat skills in the battles along the way.
One idea could be that Batman and Wonder Woman team up to face a new threat that combines high - tech weaponry and ancient magic. Maybe a villain has found a way to use old Amazonian spells with modern technology to create chaos in Gotham and Themyscira. Another plot could involve a love triangle where a new character is introduced and both Batman and Wonder Woman have complex feelings towards this person, which challenges their friendship and working relationship. A third idea is that they discover a hidden connection between their families' pasts that has been long forgotten, and this discovery changes how they view each other and their respective missions.
One plot idea could be a team - up where they face a new, extremely powerful villain that neither of them can defeat alone. This villain could have powers that are a combination of their weaknesses, like a being that can manipulate kryptonite and also has the strategic mind of Batman's enemies. They would have to learn to work together in a new way.
One idea could be that Batman and Wonder Woman have a child who inherits their combined skills. The child might struggle with the high expectations and the different worlds of Gotham and Themyscira. Another plot could be about them forming a family unit to protect the world in a new way, using both Batman's detective skills and Wonder Woman's warrior abilities.
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.
One idea could be exploring an alternate universe where Terry McGinnis (Batman Beyond) is pulled into the Injustice universe and has to deal with the morally compromised heroes. He might try to find a way to bring back the true sense of justice among them. For example, he could start by trying to reason with Superman, showing him the error of his ways through his own experiences in his own universe.
One idea could be that a new supervillain frames Batman and Wonder Woman for crimes against the world. They have to work together while on the run to clear their names. The villain could be using mind - control technology on world leaders to make them believe Batman and Wonder Woman are the threats.