In 1999, Batman Beyond introduced a new name into the Batman mythos, Terry McGinnis. Unlike Bruce Wayne, Terry grew up with a loving family well into his teen years until the murder of his father brought him to Bruce with a desire to bring the perpetrators to justice. This ultimately put Terry on a path to become the new Batman and learn the truth about his unusual lineage.
Terry's discovered who his true father was in Justice League Unlimited. In Season 2, Episode 13, "Epilogue," Terry discovered he was created using Bruce Wayne's DNA after his father, Warren, was given a flu shot that secretly rewrote his genes to replicate Bruce's. The idea was spearheaded by Amanda Waller, who realized the world would always need a Batman. However, Terry's origin was almost tied to one of Bruce's most dangerous foes, which would have made for a complicated family dynamic.
The Batman Beyond series had one direct-to-video film in 2000 titled Batman Beyond: Return of the Joker. The movie was meant to have another direct-to-video follow-up that would have revealed the film's main antagonist as Selina Kyle, aka Catwoman. She would have also been tied to Terry's birth, with creator Bruce Timm explaining, "Catwoman was going to be our leading villain in the second movie... She was the one who cloned Bruce Wayne to create Terry, but that was going to be our big surprise in our next movie." The decision to have Selina be the one to take a sample of Bruce's DNA, without his knowledge, inadvertently made her his mother.
Batman and Catwoman's relationship has always been on and off throughout the films, TV series, games and comics. Yet, Selina has always shown admiration for what Batman stands for. To have her clone Bruce's genes to ensure another Batman in the future would align with her character, considering her belief that he has an important place in Gotham and the world.
Timm's decision to make her the villain could have also been an opportunity to create a much older and layered version of Selina focused on ensuring Terry's success as Batman. She could've become an antagonist for his betterment, similar to Zoom and Wally West in the Flash comics. Not to mention a "son" born from Selina's plan and Bruce's genes would have created a twisted and powerful family reunion.
Sadly, due to the underperformance of Return of the Joker, the second film was scrapped along with the idea of making Catwoman Terry's "mother." Selina was replaced with Waller, which ultimately worked out even better. The new revelation showed Waller still took risks for humankind's betterment by implementing now illegal genetic experiments to clone Bruce without his knowledge. It also gave Terry and Bruce time to reconcile and come together as father and son, a moment long overdue.