Justice League Unlimited revisited the world of Batman Beyond twice in 2005. The first time featured Batman, Wonder Woman and Green Lantern transported 50 years into the future to stop a time-travelling villain with the help of the future Justice League Unlimited cast, including Terry McGinnis as Batman and a future Static. The second time occurred during the episode "Epilogue", where the true secret origin of the future Batman is learned in a story meant to be the de facto series finale for this Batman's story.

Set 15 years after the conclusion of Batman Beyond, Epilogue reveals that Bruce Wayne is actually Terry McGinnis' biological father. The episode is told largely through flashback sequences.

Over the years, Amanda Waller came to respect Batman and even trust him. As the years passed, she saw that he was getting older and slower. The thought of a world without Batman was unacceptable to her, so she decided to make a new one. She used her Cadmus connections to gather the technology for "Project Batman Beyond", and obtained Bruce Wayne's DNA. She found a young Neo Gotham couple with psychological profiles nearly identical to those of Bruce's parents, and injected Warren McGinnis with a nanotech solution programmed to re-write his reproductive material into an exact copy of Bruce Wayne's. A little over a year later, Mary McGinnis gave birth to Terry, a child with genetics from his mother and Bruce.

When Terry was 8 years-old, Waller employed an elderly Andrea Beaumont (the enigmatic killer from Batman: Mask of the Phantasm and once Bruce Wayne's true love) as an assassin to kill Terry's family, hoping the trauma would put him on the path to becoming Batman. However, Beaumont could not commit the act, arguing that Batman would never resort to murder to achieve his goals. Waller, however, conceded that Beaumont had been right, and made no further attempts to push Terry into becoming Batman, although she also stated to Terry that "when making a Batman, genetics is only half the story. The rest is tragedy" in an attempt to explain why she believed that doing this would put him on the path to becoming Batman. Derek Powers would later have Warren murdered, resulting in Terry becoming the new Batman. As the death of Warren proved soon afterwards, she was correct.

Fifteen years after Terry became the new Batman, Bruce's kidneys fail and doctors need a tissue donor to clone him new ones. When Terry shows a perfect histo-compatibility match with Bruce, he runs a DNA test and found out that half his DNA was from Bruce. Terry assumes that Bruce set the whole thing up, using some old Cadmus nanotechnology to have Terry's genes rewritten to match Bruce's, similar to what the Joker did to Tim Drake. He tracks Waller down, and she reveals his origins to him. Waller also reminds Terry that he is Bruce's son, not his clone, and that despite his genetics he still has free will and makes his own choice in becoming Batman.

Whether Bruce was the genetic father of Terry's younger brother Matt as well was not clearly established, as nothing was stated as to the longevity of the alterations made to Warren McGinnis; however, the series' creators have said that this is most likely the case.[8] Matt and Terry both have black hair, but are the sons of two red-haired people – a genetic improbability as red hair is recessive, and requires a gene from both parents in order to present as a phenotype.