The plot of the comic is as follows: every single bad thing that could ever happen to Superman, happens.

Bizarro loses what little sense he has and goes on a murderous rampage before killing himself, Superman's secret identity gets unveiled, causing the Daily Planet to get attacked, so Superman permanently moves to the Fortress with Lois and his closer friends. Brainiac merges with Luthor and pulls together some of the heavy hitters, and they besiege the Fortress. By the end of the siege, only Superman and Lois are still alive. Superman realizes that the only being who could have orchestrated the events was Mxyzptlk, who reveals himself and battles Superman. Superman tricks him for the last time, killing him in the process. Wracked by guilt, because not only has he killed someone, but his presence has brought death and misery to both his friends and his enemies, Superman heads into the storage chamber, permanently removing his powers before disappearing off the face of the Earth.

However, it's heavily implied that he's married Lois (who recounts the story) in disguise.

God, that was a good comic.