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".