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.
It depends on your preferences. Some people think it's great for its intense storylines and well-developed characters. Others might not be as impressed.