Sometimes, there's more than one job for Superman, and while he's on space duty, breaking up some asteroids, Batman is back on earth, dealing with Metal-Zero (Metallo). When Bruce beats Metal-Zero, he has Clark, who just showed up after dealing with the asteroids, clean up. Though, soon after Bruce leaves, Metal-Zero disappears right in front of Clark's eyes.
Turns out Metal-Zero isn't real! He's a video game avatar that manifests himself into the real world thanks to the Toymaster and his engineer Agnes. As they plan to up the game so to speak, fragments of the asteroid Clark busted up fall through the atmosphere, and uh-oh, Black Mercy flowers spawn and releases spores all over the world.
While Bruce trains, and Clark finds out that Metal-Zero has been under US Army lock up, Hiro gets some new players into his game, one of the best gamers on the planet, a fellow game designer, and Jimmy Olsen, who is rich and an investor in the project. All of them go into the game thinking it's just that, and don't quite realize that their game's goal of "killing Batman" actually manifests in real life.
Later, Clark tells Bruce about Metal-Zero, which leads Bruce to go back to investigate the scene on his own, refusing Clark's help. Bruce finds Nightwing at the scene, and the two go right into investigation mode, but Bruce soon figures out it's not Nightwing, when he's attacked, followed by Nightwing flying away after he fights back.
With "Nightwing" being controlled by Jimmy and the other players, they're pretty entertained by the "recreation" of Gotham, and end up back in Toymaster's workshop, where he tries to tell them that he's real and not part of a game, which Jimmy finds to be the lamest meta story he's ever heard. Nevertheless, Bruce shuts the game down, and plans on destroying the console... though Agnes has another plan, and she might not exactly be real.
BUT BOOM, Oh shit, it's Mongul, who apparently tried to take over the earth a few years back (was that the villains month issue? didn't read it) and failed, surprisingly. But this time he's back, and he studied the earth, realizing there were millions of soldiers he could take control of who spent billions of hours practicing fighting and tactics... You know, VIDEYA GAMES!
One laser to the chest later, and Bruce is calling out for Clark's help.