Well, the 'Injustice: Gods Among Us' comic full story is centered around Superman's transformation. When the Joker plays his cruelest trick on Superman, it sets off a chain of events. Superman starts to believe that only his way can bring true peace and justice. He forms a regime. Batman, on the other hand, is against this new order. Many characters get involved, like Wonder Woman who initially supports Superman but later has doubts. It shows how far the heroes can be pushed and how their ideologies can clash in a world that has been turned upside down by a single act of evil.
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.
A good plot for Injustice Gods Among Us crossover fanfiction could be a time - travel - based crossover. Maybe a character from Injustice accidentally travels to a different timeline in the DC universe where things are much more peaceful. This character would then have to adapt to this new world and its heroes and villains. Or perhaps characters from different eras of DC, like Golden Age heroes, cross over into the Injustice universe. They would be shocked by the state of the world and try to bring back the old values of justice. They could team up with some of the Injustice characters who still hold onto those ideals.
The main plot point is the Joker's manipulation that leads to Superman's downfall. Another is Superman's establishment of a regime. And Batman's resistance against it.
The story might involve a powerful being with god-like abilities showing up in our world and causing all sorts of changes. The theme could be about power, responsibility, and how humans react to such an extraordinary presence.