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.
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.
Superman would be extremely interesting. In the Injustice universe, Superman has become a dictator of sorts. Terry, as Batman Beyond, represents a different kind of heroism. Their interaction could be a clash of ideologies. Terry would likely be appalled by Superman's actions and try to make him see reason, which would lead to some intense and thought - provoking exchanges.
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.
It could be shown as a very strained relationship. For example, Wonder Woman might initially be very hostile towards Batman, seeing him as a threat to the order Superman has created. But as time goes on, she starts to see the value in his approach. There could be many tense confrontations between them that gradually turn into more respectful exchanges as they understand each other better.