Alan Moore, the writer of the story which this episode is based on, notoriously despises and discourages film and television adaptations of his works. However, according to Bruce Timm and Dwayne McDuffie, Moore confided that he was in fact pleased with the result of this episode. Notably, he allowed himself to be credited in it, which is rare. This is one of only two adaptations of Moore's work that Moore himself approved of, the other being the YouTube parody Saturday Morning Watchmen (2009).
The story is derived from the celebrated comic book story of the same name in "Superman" (vol. 1) Annual #11 by Alan Moore and Dave Gibbons. With the author's permission, the JLU creative team made several key changes: Kal-El's "wife" is Loana, a merger of Lois Lane and Lana Lang, with Lois's voice, rather than Lyla Ler-Rol; Kal-El's "daughter" Orna is omitted; The comics story had Kal-El's "dream" Krypton depicted in more detail, and featured a subplot of a rebellion against society involving Jor-El and cousin Kara; Viewers do not get to see Mongul's fantasy as it was depicted in the comics: he imagines killing Superman and all of the heroes, and ruling over Earth - creating a new War World. This is hinted at by the end of the episode, when the audience hears screams of pain and terror from inside Mongul's head.
The pre-Crisis Jason Todd Robin was in the original comic book story. It is he who attacks Mongul with the Black Mercy instead of Wonder Woman.
Jor-El's appearance is similar to Superman's design in Season 1 of Justice League (2001). Some fans disliked the additional lines on Superman's face that were supposed to make him look chiseled, instead claiming it made him look 20 years old than he did in Superman: The Animated Series (1996). Producer Bruce Timm stated on the DVD commentary that this is an intentional gag.
When the Black Mercy attaches itself to Batman, he dreams of leaving a movie theatre with his parents as a young boy. The movie title on the marquee, was "The Mark Of Zorro." The character Zorro, was actually the main inspiration behind the Batman character that Bob Kane created. (Both characters are rich playboys who don a black costume to fight crime.)