Here’s my idea for a story:
It takes place after Superman’s ending. Most of the heroes and villains are being mind controlled by Superman and his regime, but there are also some heroes and villains who willingly work for Superman to keep their free will. The few remaining rebels (I would include Green Arrow as a rebel) are working on rescuing an important prisoner (possibly Barbara Gordon?) to help them restore Brother Eye. They use Brother Eye to contact another dimension (the same one they contacted in the first Injustice) to help them fight Superman. The Justice League from the alternate dimension and the rebels team up to take down Superman, which they eventually do successfully. However, this was all part of Brother Eye’s master plan! It’s become sentient, and now that Superman’s out of the way, it takes over the mind controlled heroes and villains. The Justice League & rebels lose a few members (who are turned into mind controlled slaves), but the members of the regime who retained their free will join the rebels. They then have to fight Brother Eye and it’s army.