if I was going to rewrite Injustice (not that anyone asked) I would make Lex Luthor the primary (accidental) antagonist who tries, in a last-ditch effort, to covertly infuse his final stores of Kryptonite (the ones he saved from Batman's search that are barely enough to make Clark a little queasy) into Lois Lane, with the primary goal of delivering a stronger dose via saliva/other bodily contact. not enough to harm Clark, and it won't harm Lois, but it'll mean Superman can't kiss his wife or spend time near her without weakness, something he'll exploit in a later plan (somehow).
except it goes horribly wrong, because Lois is pregnant with a half-Kryptonian child. and all of a sudden, Lex Luthor has a murderous Superman hunting him down, not realizing that he'd inadverdently tipped the same scales Joker did in the primary Injustice universe. a simple dose of Kryptonite took Lois and the unborn baby out; it made it so her corpse was so saturated with Kryptonite, Clark couldn't even bury her on his own or carry her to help.
then. then, Bruce steps in. without Joker, without a missing Metropolis, forced to hold his friend back from vengeance and protect Lex Luthor from Superman. the primary conflict is over Luthor. Clark is horrified that Bruce would spare his life, of all people. and it's worse than Joker because Luthor's motivation wasn't madness or chaos. it wasn't even to harm Lois, and he's shaken by the results. he poked at Superman and the only thing holding the gaping maw of his anger back is an unlikely ally...Bruce Wayne.
the rest of the JL folds in around that conflict and the ensuing keep-away game.