As Brainiac pulls back to regroup his forces, the Justice League and Lex Luthor attempt to discern clues as to his location in his downed Skull Ship. Splitting into two groups; one investigating the bottled cities and one investigating the ship, the former group encounters new armies who had allied with Brainiac during his past alien takeovers. The latter group discovers evidence that Luthor had been thoroughly involved with Brainiac's invasion; moreso than just designing the Enforcer robots.
Although it was a ploy by Brainiac, the revelation effectively drove the JLA into believing Luthor was against them. Meanwhile, the armies of the Bottle Cities escape onto Earth to wreck havoc
"Excuse me? I've always been against extra-terrestrials who come to Earth declaring they are the saviors of humankind. And I am still against people in masks telling those of us who show our faces what is right and wrong. I will not apologize for putting mankind first." — Lex Luthor