I doubt it's the Atom because I find it hard to believe that Meltzer would reveal the mastermind at this point of the series. He seems to have a penchant for misdirecting the reader and I question if he's doing that again.
Plus, seeing as how DC is bringing back Hal Jordan and ending any possibility of him becoming Paralax again it's difficult to believe DC would go down the hero-turned-villain road again after taking heat for Paralax.
I question if we'll EVER learn who the mastermind is, which would be an interesting twist. In the real world, there's always unsolved murders. Why not in comics?
Also, I think in the last issue Brad will want to show the consequences of the JLA's actions with Dr. Light and Batman. What might be possible is Batman subconsciously manipulating the Calculator. The Calculator has stated he's been paid for all of this, and Wayne Enterprises certainly has the money. After seeing the protocols he set up to take down the JLA as well as the gangs in Gotham City in the recent Wargames arc it's entirely possible Batman's behind this. Motivations? Not much, but again the moral of the story would be that the JLA can't play God.
What's the Atom's motivations? I can't come up with any.
"You kind of get tired giving the other team credit. At some point you've got to look in the mirror and say 'I sucked.'"
Alex Rodriguez, after the NY Yankees were eliminated from the 2006 ALDS by the Detroit Tigers.