My guess from the way things have been depicted so far is that they will encounter each other while investigating the boxes (which I'm guessing could be micro boob tubes or tesseracts of somekind) while ruffling each others feathers along the way while learning to work together to solve the crisis at hand. Then after they are together they decide they can work together and form the Justice League. I'm guessing they nominate Superman as their leader and Bruce will give his "Gotham gets my priority but alert me if there is something actually seriously you need my help with and maybe I'll aide you guys" speech. Then the second arc flash forwards to the present and we see how the roster has expanded, etc.
Actually as much as I'm enjoying this new, harder-edged take on Superman, I'm having a hard time imagining him being the "leader" of the Justice League now. He just seems like too much of a loose cannon.
To me, Batman would be the more obvious choice, being clearly the most adult
person in the group.