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 devised a scheme 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 (easily accomplished as he was often treated by emergency personnel for minor wounds after battles), a young couple was found that were almost identical psychological matches to Batman's father and mother: Warren McGinnis and Mary McGinnis. During an apparent routine flu inoculation, Warren was administered a nanotech solution that over-wrote his reproductive DNA with Batman's. A year later, Terry McGinnis was born as a genetic son of Mary and Batman.
Knowing that genetics were not the only factor in creating Batman, Waller later hired an assassin to murder Terry's parents at the same age and under very similar circumstances as his predecessor to try to recreate these conditions. The hired assassin, knowing what the murders had done to Batman and realized that she would be dishonoring everything he stood for, refused to subject another child to the same horrors. When Waller realized she had gotten too far, she scrapped the project.
Shortly after the failed assassination, Warren and Mary had another son.
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.
At some point after Terry became Batman, Bruce became aware of their genetic relationship. He concealed it from Terry, feeling that Warren had raised Terry and so deserved to be remembered as his true father. He also wanted Terry to be his own man and not to feel that his fate had been ordained by his birth.
When Bruce began to suffer from 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. Surprised, Terry ran a DNA test and found that he was Bruce's genetic son. Initially believing that Bruce had been behind the scheme, Terry sought out Waller 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. Armed with this reassurance, Terry freely chose to carry on as Batman.
- The fact that Bruce Wayne became aware of his and Terry McGinnis's lineage but chose to keep it secret was explained in background by Dwayne McDuffie.
- 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.