Mageddon was created by the Old Gods, the predecessors of the New Gods of the Fourth World, as one of the weapons that led to their destruction; according to Orion it was the direct cause of the destruction of 'Joyous Home', the star-city of the Old Gods. It survived the war and was imprisoned at the edge of space-time in a gravity sink. During the 15 billion years it spent in hibernation the multi-planetary fortress called Wonderworld was erected to watch over its slumber, manned by the "superbeings of ten thousand worlds".
Mageddon's infamy extended beyond the survivors of the Old God's Ragnarok and the denizens of Wonderworld. Knowman was attempting to prepare the world for this cosmic threat when he encountered the JLA. Zauriel was assigned to Earth specifically in anticipation of Mageddon's coming; similarly, the Q Foundation prepared for thousands of years in training Aztek and his predecessors.
Mageddon escaped, destroying Wonderworld effortlessly in the process, and headed for Earth. Orion first deducted its coming by the remote emissaries it sent to antagonize Earth's criminals. They influenced jail riots around the world and more subtlety arranged the formation of a new Injustice Society. Luthor, General Eiling, Prometheus and Queen Bee were driven to attack the JLA to erase any organized resistance.
In a desperate gamble Superman and Orion use a Boom Tube to teleport themselves into Mageddon's heart. Unfortunately Orion was nearly killed and Superman chained as its mental slave. Aztek managed to find the two even though he had lost his eyesight. He healed Orion and then detonated his 4-D mirror to hurt Mageddon internally. The civil wars on Earth were stopped by Zauriel and the hosts of the Pax Dei while Glimmer (the last survivor of Wonderworld) powered re-purposed Purple Ray technology to accelerate the evolution of humankind into superhumans. These people and the Pax Dei attacked the machine head-on in space. As a last resort Mageddon attempted to detonate its core, which would destroy half the galaxy. Fortunately Superman broke its mind control and used his body to absorb the anti-sunlight energy, shutting it off.
Mageddon itself is an enormous engine of destruction that dwarfs the Earth-moon system in size. Its primary power is to invoke aggression and hate among sentient creatures by stimulating the basal ganglia. Mageddon's effects are felt on a planetary scale and succeeded in making Wonderworld's heroes kill each other. It can also control individuals by stimulating all their negative emotions simultaneously: fear, despair, self-loathing, etc. The machine has control over its own structure and creates mindless drones to carry out its basic functions.
Mageddon is able to create "remote transceivers", large eyeballs made of flesh, which latch onto people and allow Mageddon to influence certain areas psionically from a vast distance. These eyes can shoot powerful energy beams as a defensive measure.