During encounters with the Justice League, both hostile and friendly, Amanda Waller developed a great admiration for Batman and came to believe that someone like him would always be needed. As she watched Batman age, she realized he wouldn't be around forever and the Dark Knight would have to retire or someone would finally kill him. Drawing on her old Cadmus contacts, Waller gathered the technology needed to give Batman a genetic "son" who would likewise be compelled to take up a life as his successor.
After obtaining a sample of Batman's DNA, which was easily accomplished as he was often treated by emergency personnel for minor wounds after missions, Amanda found a young Neo-Gotham couple with almost identical psychological matches to Batman's father and mother: Warren and Mary McGinnis. During an apparent routine flu inoculation, Warren was actually administered a nanotech solution that overwrote his reproductive DNA with Bruce Wayne's. A year later, Terry McGinnis was born as a genetic son of Mary and Bruce.
Knowing that genetics were not the only factor in creating a Batman, Waller later hired an assassin to kill Terry's parents at the same age and under very similar circumstances as his predecessor to try to recreate these conditions: With an 8-year old Terry witnessing his parents' murders after watching a movie. The hired assassin however, backed out at the last minute, realizing that she would be dishonoring everything Bruce stood for by subjecting another child to the same horrors. When Waller realized she had gotten too far, she canceled the project.
Shortly after the failed assassination, Warren and Mary had another son, Matt McGinnis, a by-product of the project.
Project Batman Beyond was ultimately successful despite Waller's abandonment when Terry had a chance meeting with Bruce Wayne, Warren was murdered on Derek Powers's orders, and a new Batman was formed.
Bruce later became aware of his genetic relationship with Terry, but chose to hide it from him, feeling that Warren had raised Terry and deserved to be remembered as his true father. Bruce also wanted Terry to be his own man and not to feel that his fate had been dictated for him by his genes.
When Bruce suffered a kidney failure, Terry was checked for compatibility of being a tissue donor to clone the organs needed and was found to be a perfect match. Disturbed, Terry ran a DNA test and found that he was Bruce's genetic son. Though initially believing that Bruce had been behind this, Terry sought out Waller, the only person with the acumen for making genetic experiments, for answers. Waller then explained the truth to him and told him that he was not Bruce's clone but his son - his own man free to choose his own path in life, although she advised him not to distance himself from his friends and loved ones as Bruce had done. With a new sense of purpose, Terry freely chose to carry on as Batman.
- Project Batman Beyond's plan is a good example of the dichotomy of Amanda Waller's character: she is willing to use the most terrible and unscrupulous means but in pursuit of goals which she considers right and for the greatest good.
- There are strong similarities between Project Batman Beyond and the scheme formed by the fictional version of Dr. Josef Mengele in Ira Levin's novel The Boys From Brazil. In that novel, Mengele attempts to create a new world leader like Adolf Hitler by creating multiple genetic clones of Hitler, then trying to influence them in the same direction by placing them as infants with foster families of similar backgrounds, and arranging for their fathers to be killed at the same age Hitler's died. In what is probably a nod to this, one of the headings in Project Cadmus's computer files stolen by Question in the Justice League Unlimited episode "Question Authority" was titled "Brazilboyz".
- "Project Batman Beyond" is an in-universe reference to the Batman Beyond series.