In the opening scene a good version of Lex Luthor, along with a good version of The Joker, known here as The Jester, steal a quantum trigger device before an evil version of the Justice League apprehends them. Luther escapes when the Jester sacrifices himself. Luthor appears on another Earth, goes to the nearest police station and asks for them to contact the Justice League. Immediately Superman sees that he's from another Universe, as his internal organs are reversed. Luthor asks for the team's help to defeat the Crime Syndicate, which is led by Ultraman. During this adventure the Martian Manhunter develops feelings for the President's daughter, though they can never be together. Owlman, sort of an evil Batman, wants to find and destroy Earth Prime, the first and original Earth upon which all the others are copies. So the fate of the worlds depend on a battle between Batman and Owlman.
This is a good continuation of the JLA animated series, though I thought it was funny that all the evil versions of the characters have accents, like Ultraman with a thuggish Brooklyn accent, the Flash counterpart sounding Australian, et cetera.
Written by Dwayne McDuffie, who penned may of Cartoon Network's JUSTICE LEAGUE series stories.