^Sorry if I spoiled anything for you.
It wasn't revealed that Bruce was Terry's biological father until the Justice League Unlimited episode "Epilogue", which takes place 15 years after the conclusion of Batman Beyond.
Amanda Waller decided that the world needed Batman, and when she saw that Bruce was slowing down/getting older she decided to make a new one. The name of the project to make a new Batman was "Project Batman Beyond". She got Bruce's DNA from the battlefield. She found a young couple with psychological profiles nearly identical to 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. Making Bruce Terry's biological son.
Years later Waller sent the Phantasm (Andrea Beaumont, first seen in Batman: Mask of the Phantasm) to kill Terry's parents. She thought that tragedy was the second half of the equation to making a Batman. The Phantasm couldn't go through with it, and Waller decided that it was wrong to kill the parents. Derek Powers (Bruce's business partner) would later have Terry's father murdered, resulting in Terry becoming the new Batman.
Last edited by Batman25JM on Mon Jun 14, 2010 7:27 pm; edited 1 time in total