HAHA From Wikipedia:

"In #14, he is confronted by Superman-Prime. In issue #13 Superman-Prime fights with Monarch, becoming slightly injured after Monarch exposes part of his suit. In a fit of rage, Superman-Prime redoubles his attack on Monarch and while his temporarily Oan Guardian-boosted powers begin to fade he rips open the chestplate of Monarch's containment armor, resulting in a huge explosion of quantum energy that devastates the entire universe of Earth-51. While Superman-Prime was later found lost in time by the Time Trapper, and sent to the 31st Century, the status of Monarch remained unknown. An amnesiac Captain Atom has resurfaced some time later in Superman's Pal: Jimmy Olsen Special #2 (2009); Action Comics #880 establishes he has no memories of his actions during Countdown, and has to confront a resurrected Major Force in #883. He subsequently embarks on a path of redemption."

In other words DC thought it was a great idea to finally make Captain Atom, The Monarch. But when it didn't work out they gave the character amnesia in hopes that it would give the readers amnesia as well.