The story opens with Superman struggling with the fact that he could not save all the people that were caught in The Vanishing. He visits Father Leone, a priest suffering from cancer, in his church. Superman tells him how he was in outer space saving Green Lantern Kyle Rayner when The Vanishing occurred, outlining his feelings of guilt as he feels he abandoned Earth when it needed him most.
This is a first of several 'confessionals' between Superman and Father Leone. At their next encounter, Superman explains how he traced the source of The Vanishing to an unnamed foreign country in the Middle East. In the midst of a war, Superman removes from one side all of their weapons; on the other he faces General Nox, a military leader intent on taking over the country. Nox refuses to stand down and, along with his super-powered minion Equus, fights against Superman's interference. Equus is injured and, in a last-ditch attempt to escape, activates the Vanishing Device, creating a second "Vanishing", which vanishes himself, General Nox and 300,000 more inhabitants of Earth. This leads to Superman having to face the anger of the public and the JLA.
Taking control of the Vanishing Device, Superman and Father Leone travel to the Fortress of Solitude, where they try to perfect the device so that Superman can vanish himself to discover where the other people were taken. Before he gets a chance to do so, he is confronted by Wonder Woman, who attempts to stop Superman from carrying out his plan.
