WARNING what i'm obout to tell you is a SPOILER if you havent seen
Batman V Superman dont read on well its up to you........

in Batman V Superman theres a short scene where it shows the Flash either from a different universe or from the future timetraveling to tell bruce obout how he was right obout how superman was bad and that louis lane is the key he then says hes to soon and stuff and gets pulled back to either his universe or back into the future but before he goes he says "you must find us bruce"
in my opinion this means he is with the justice league.
the whole thing obout superman being bad is like injustice gods among us where loise lane is dead and superman turns evil and kills off the justice league so thats my opinion whats yours say it in the comments below