Something is wrong with Batman, and Superman need's SHADE's help, more specifically, needs SHADE scientist Ray Palmer's help. After traveling to the floating Ant Farm to retrieve Palmer, Superman brings the scientist to the Fortress of Solitude where there's a comatose Batman, and what looks to be a dead microscopic superhero in his blood... So, time to go inside Batman's brain, and figure out what's wrong.
Turns out after an adventure into space to fix a satellite, a microscopic space ship, with a whole kingdom inside it, found its way into Batman's blood, and is resting in his brain. Shit's gone bad on the ship, as some villains of the alien race have taken over, and obviously start fighting Superman and the soon-to-be-called Atom.
One of the alien grabs on to Superman's shrink belt, mistakenly believing it to be the source of his power, enlarges himself, and ends up outside Batman's body at full size. While Superman and Palmer are still inside Batman's brain, they manage to defeat the other bad guy, and begin to dislodge the ship, allowing Batman to wake up, and kick the other guy's ass, despite having a serious headache.
When all is said and done, Palmer puts the ship into a portable Ant Farm that he'll bring back to SHADE, and he along with Superman exit Batman's body, of course, not to Batman's liking. Batman isn't exactly sure about having SHADE inside of him so to speak, but Superman seems to trust Ray, and Ray seems to be a trustworthy guy.
When Ray leaves to go back to SHADE, Batman and Superman talk about SHADE and the possibilities of the Atom, referring back to Atomica of the Crime Syndicate. While they're right to trust Ray, Batman was right not to trust SHADE, as unbeknownst to Ray, Father Time, SHADE's leader, dispersed micro tracking technology in both Batman and Superman's bodies... UH OH.