The Reign of Emperor Joker

This was a big month, kicking off with a double-sized special and ending with a double-sized finale.  Emperor Joker was an imaginative story that's fun to read over and over, and while it introduced some new characters who would pop up occasionally during the Loeb era, it didn't really have many lingering ramifications.

Superman: Emperor Joker #1

On Earth, Emperor Joker holds court with Harley Quinn and other characters under his control, like Lex Luthor and the Riddler.  Curiously, he doesn't seem to have any recollection of creating the new villain Ignition.

On the moon, Superman learns that when Mr. Mxyzptlk got bored with annoying him every 90 days, Mxyzptlk tried to have some fun with the Joker.  However, he discovered that just because the Joker was criminally insane he wasn't stupid, and the Joker ended up stealing all of his power and re-made the world in his own image.

Accompanied by Lois Lane, Steel, and Supergirl, the Man of Steel seeks help from his friends in the JLA.  Still influenced by the Joker, all of his friends are now comical parodies of themselves.  Wonder Woman is a domineering housewife, the Martian Manhunter resembles Marvin the Martian, the Flash is fat, Aquaman is half fish, and Green Lantern is now the Yellow Paper Lantern.  Superman wants to know what happened to Batman but Mr. Mxyzptlk dodges the question.

Superman gives an inspiration speech and Lois, Steel, and Supergirl remember who they are and are restored to their original selves.  Lex Luthor yells at the Joker for letting Superman give his friends hope, so the Joker kills Lex.

Superman #161

This says it's The Reign of Emperor Joker part 6 even though the preceding issues were not titled parts 1-5.

Superman leads a stealth underwater attack on the Joker's Gotham City lair with Lois, Steel, Superboy and Supergirl.  The others don't trust Lois Lane but Superman defends her.  She tells him he doesn't have to stand up for her and kisses him as proof.  However, when Lois gets inside the Joker's hideout without the others, she offers to make a business proposition.

Team Superman gets distracted by the Joker's minions, Bizarro, Bounty, and Ignition.  After evading the villains, Superman finally finds out who has been screaming every night when he finds Batman's corpse nailed to a wall.

Adventures of Superman #583

Superman gives Batman's body a proper burial, writing "Batman: A True Hero" on his tombstone.  But as seems to happen every night, Batman comes back to life and digs himself out of the grave.  Superman and Batman are then attacked by an army of zombie clowns who emerge from the ground of the cemetery chanting the 60's Batman theme.

When the heroes regroup to attack the Joker, they find he's taken Lois Lane prisoner.  However, when Superman tries to save her she betrays with a Kryptonite ring.  The Joker transforms Lois into his empress and turns the heroes into the Super Pets, revealing his next plan is to destroy the whole universe.

This is the first post-Crisis appearance of the Legion of Super Pets, with Supergirl as Streaky the Supercat, Batman as Ace the Bathound, Superboy as Beppo the Super-monkey, Steel as Comet the Super-horse, and Superman as Krypto.  Though this Krypto would not carry over from this story, a real version of him would be re-introduced 6 months later.

Superman: The Man of Steel #105

The Joker forces Batman to watch a movie in which Superman finds himself in the role of Bruce Wayne on the night of his parent's murder.  The movie continues where Superman finds himself as a cartoonist who makes an unapproved drawing of the Justice League as they really are.  Superman refuses to follow the Joker's script and ends up in limbo with the Spectre, who at this time was former Green Lantern Hal Jordan.  Superman asks why the Spectre hasn't tried to stop the Joker himself, but even the almighty Spectre is taken over by the Joker's power.

The Justice League watches the show on TV and when they see Superman's drawing they turn back into their regular selves.  Wonder Woman tells her teammates to prepare to storm Joker City.

Action Comics #770

Unfortunately, the Joker kills the entire Justice League instantly.  The Joker leaves Superman and Batman hanging to a wall, with Batman's mouth sealed shut.  In morse code on his teeth, Batman tells Superman to kill the Joker, but Superman still wants to find another way even as the Joker has Batman eaten alive by vultures.

Harley Quinn asks the Joker why he has to end the world, and he tells her how in a twisted way his destruction will have a healing effect, leaving behind a blank slate where somebody like him won't ever come into existence.  Although she's been replaced by Lois, she begs him to spare her and he turns her into a constellation so she'll have the best view of the end of the world.

The Riddler noticed that the Joker didn't seem to have created Ignition, so he gets him to attack the Joker theorizing that Ignition is the one person whose mind the Joker can't read.  Unfortunately, the Joker survives Ignition's blast.  

Empress Lane asks Superman if he can stop the Joker.  He tells her he doesn't know, and she admits she doesn't believe he can, but she begs him to make her believe.  The Joker kills Lois for her betrayal, but before she dies she returns to her regular form and thanks Superman.  Superman and the Joker engage in a cosmic, planet-shattering battle, but Superman wins by making the Joker realize he can't erase Batman from existence because he can't get Batman out of his head.

Mr. Mxyzptlk and the Spectre put the world back together, although Mxyzptlk has made a secret bargain with Ignition that will let him stay around beyond this story.  Batman's mind has been completely shattered from dying infinite deaths, and Superman asks the Spectre to transfer the memories of those deaths to his mind instead to save his friend's sanity.  This era was characterized by Christological sacrifices over traditional heroism, but although this particular act resolves the story arc it's never really mentioned again.