According to writer Dwayne McDuffie, Bruce, as the world's greatest detective, was aware that Terry and Matt are his genetic offspring some point after Terry assumed the role of Batman and realized the machination of Amanda Waller and Project Cadmus, but would never bring it up as he wanted Terry to be his own man, and out of respect for Warren McGinnis as well since he was the one who raised him since birth.
Dwayne McDuffie confirms the setting to be 15 years after the end of Batman Beyond (1999), which. Bruce Timm gives this as 50 (not 40 as some claimed) years in the future from when the audience is watching it.
The new Royal Flush Gang bear specific in-joking in each of their identities: Ten has a white swimsuit and blond cornrows just like Bo Derek in the movie 10 (1979); Jack is a samurai, thus putting a spin on the Cartoon Network character Samurai Jack (2001). When this character is returned to normal, he bears a resemblance to Phil LaMarr, who voices Samurai Jack; Queen bears a resemblance to the Queen of Hearts from Lewis Carroll's Alice in Wonderland. When this character is returned to normal, it is revealed to be a man, thus a "drag queen"; and King looks like MODOK, a Marvel Comics character created by Jack Kirby (Whose's nickname was "The King").
The trivia item below may give away important plot points.
This episode used story elements from a Batman Beyond movie that would have had Selina Kyle/Catwoman as the person responsible for the cloning of Bruce Wayne instead of Amanda Waller resulting in Terry and another, whose anti-hero personality would result in his fall from grace after he began to cause the death of Batman's enemies. Due to the dark tones of the plot and controversial reception of Batman Beyond: Return of the Joker (2000), however, the movie was rejected. During production of the episode, the creative team decided to tie it in with the Cadmus arc.