Kingdom Come

Promotional Art for Kingdom Come

Plot

10 years prior to the story, the Joker killed the staff of the Daily Planet. He was sent to trial, but a new superhero called Magog killed the Joker and people called him a hero. Upset that the public is treating this murderer as a hero, Superman withdraws from world at large. Due to Superman not being a role model for superheroes anymore, superhumans simply battle each other without cause or concern for the bystanders.
Impending Disaster

The story is told from the point of view of Norman McCay, who gains from the Sandman the ability to see into the future. With the help of the Spectre, he jumped through time and space to see what's happening. Magog's Justice Battalion tried to kill Parasite, but Parasite tore Captain Atom open... causing an explosion and killing millions of people.
Second Coming of Superman

Superman finally decided to come back and try to stop the rogue superhumans. He reformed the Justice League to include some of the "old" heroes (Green Latern I, Hawkman, Dick Grayson [now called Red Robin]) and reformed superhumans like Avia (daughter of Big Barda and Mr. Miracle). However, Batman thought that Superman was being too idealist and formed the Outsiders (which consisted of non-powered heroes [such as Green Arrow] and second and third generation heroes). Lex Luthor formed the Mankind Liberation Front (consisting of Silver Age villains and third generation villains).

Pact

The Justice League created a superhuman prision, but it was filled up within two weeks of its creation and pressure built as the superhumans started riots. Meanwhile, Batman discovered that Lex Luthor has brainwashed Captain Marvel. The prisoners of the before mentioned prison killed Captain Comet and Captain Marvel frees them. This leads to the JL and the rogue superhumans to clash.
Armageddon
While things get worse, the U.N. decided to nuke the superhumans. Wonder Woman and Batman stopped two of the planes with the bombs. But, one got pass them. Meanwhile, Superman and Captain Marvel clash. But, Superman managed to free Captain Marvel from the brain washing. Captain Marvel used his lightning bolt to cause the bomb to explose in mid-air, but it killed most of the superhumans.(Green Lantern managed to save a few) Superman went mad and runs amok (he thought everyone else died). However, Norman talked him out of this saying this was why humans fear the superhumans.
Epilogue
Batman opened up a hospital for the superhumans harmed in the previous battle and Superman restores the farm lands destroyed by Captain Atom exploding.

References

http://en.wikipedia.org/wiki/Kingdom_Come_(comics)