Originally, it was Selina Kyle, not Amanda Waller, who had helped create Terry and in fact several other clones of Bruce Wayne in order to become the ideal crime fighter.
“Staying much closer to the Boys from Brazil set-up, Selina hedged her bets and created lots of Bruce Wayne clones, and systematically murdered their parents when they reached the proper age. Most of them didn’t become manic-depressive crime-fighters, only Terry and one other—a young boy she adopted and raised as her own son. There was going to be a creepy ‘Manchurian Candidate’ aspect to their relationship, with the aging (but still disturbingly kinda sexy) Selina coaxing the kid into becoming an über-messed-up avenger of evil.”
The ‘son’ of Catwoman would be the main adversary for Terry and was in his own ‘dark superhero’ costume. Most of the movie he was hunting down the Batman Beyond rogues gallery and even classic Batman rogues like Edward Nygma, though Timm admitted he felt this was too ‘Phantasm’ for him. During this, Terry would discover his origins and break up with Dana, who is trying to hint to him about possibly typing the knot after they graduate when they’re at one of her cousin’s weddings. Distraught and worried about the bad guy hurting Dana or one of his rogues, Terry breaks up with her.
“This version of Selina had, at some point in the past, ‘seen the light,’ after years of Batman nagging her to use her talents to help people instead of just helping herself. She eventually realized he was right, but with ‘born again’ zeal, decided Batman himself didn’t go far enough in punishing criminals; she needed a Batman who would help her eliminate criminals (i.e. kill them dead) and set about creating one. These were going to be ‘true’ Bruce Wayne clones, not nano-engineered ‘sons’“
However several plot holes were pointed out such as how Selina could manage this plan as she was not a scientist or had the resources to use this. Along with this, many members of the staff felt this hit too many similar plot beats to Return of the Joker. Dwayne McDuffie eventually created the means of the artificial DNA rewriter from Cadmus and with his help, they were able to put this at the end of the Cadmus mini-arc that had been the focus of the show.
Still, there were still some more changes. An idea was toyed around with that Waller had also created several other ‘Batmen Beyonds’ along with Terry. Any girls would live their life normally while boys in good health would have the same tragedy that Bruce endured. Eventually, it was dropped to just Terry’s family.
The final product has a few traces of the original idea, such as Terry and Dana ‘breaking it off’ in Terry’s mind only to go ahead and get married at the end. Terry’s (and by extension Matt) origin remained the same, though with the change that Terry was the son of Bruce as opposed to a clone. Terry also dealt with the idea of being cursed as being Batman throughout most of his time upon learning the truth.
There is one interesting note however about the original idea. Several years later, the idea of a genetically created dark avenger going around and killing Batman’s rogues gallery both original and new was utilized in the Adam Beechen 2010 mini-series, Hush Beyond. Whether this was an intentional nod by Adam Beechen is unknown.