According to Bruce W. Timm, originally this episode was a turning point for Batman, and he was originally going to split off from the League and join Cadmus. Since there was no way to do this without making Batman look like the bad guy, the idea was scrapped. Timm has stated that if the plan came to fruition, Batman would have created a superhero team of non-super powered heroes, such as Huntress and Wildcat.
According to Dwayne McDuffie, Hugo Strange's cameo as one of the departmental heads of Project Cadmus was a set up for a later appearance (presumably the Question interrogation scene in "Question Authority"). However, because of the Bat-Embargo, the character became off-limits, so they used Dr. Moon instead.
The events in this episode are the possible impetus for Batman creating a contingency plan to stop the Justice League members by exploiting their weaknesses, as seen in the movie "Justice League: Doom".
Doomsday's origins are explained as him being a creation of Cadmus. When the character was originally introduced in the comics, none of the heroes could determine his origins; yet many mistakenly believed him to have been Cadmus' creation.
The character Doomsday, was originally introduced in the comic series, "The Death of Superman." Unlike his depiction in the television show, he was not a creation of Cadmus. Doomsday actually comes from Krypton. Thousands of years before the time of Superman, a "child of the planet" was selected by Kryptonian scientists to be engineered as a weapon. He was subjected to torture and mind manipulation until he perished; and was brought back to life again and again. This process was repeated for years, in order to create a berserk, raging creature that can return from any kind of death. The result was, the immortal monster that landed on earth and eventually killed the man of steel. Doomsday cannot be killed the same way twice and will regenerate from any death.