Death

Warren worked at Wayne-Powers as part of the research division. He met with Harry Tully, who gave him a disc containing data on the under-the table nerve gas being produced for for Kaznia despite a weapons embargo being in place for that region. Harry was interrupted before he could explain what was on the disc by Mr. Fixx, who takes Tully away with armed guards. Warren is then summoned by Derek Powers, who explained that Harry was having an allergic reaction to one of the chemicals they were producing. When asked if he knew the location of the disc, he expressed no knowledge of it.
 
At home, after examinining the disc, he and his son Terry, who is living with him, get in an arguement which ends with Terry stroming out of the house though he is ground. This would be the last time Terry would ever talk to his dad. 
 
Terry goes out with Dana Tan (his girl friend) to party, but is interrupted by the Jokerz. A fight breaks out and in the end, Terry runs for his life. He met Bruce Wayne and the two defeat the gang.
 
Upon his return, he finds the house surouded by police. He sees his mother, Mary McGinnis , who explains that the police are blaming it on the Jokerz. He rushes inside. Warren McGinnis is dead.
 
Terry later finds out, by over hearing Mr. Fixx talking to Powers, that Fixx "took care of his [Terry's] old man".  In the end, Terry is able to defeat both Powers and Fixx.
 
 
 

Project Batman Beyond

Terry later discovers the shocking truth about his parentage. When Bruce requires tissue for the cloning of a kidney to transplant, Terry is checked for compatibility, and to his surprise, his DNA is similar to Bruce's. After hesitating for a time, he runs a DNA test and finds out that Bruce is his biological father. Terry accuses Bruce of orchestrating his entire life and even contemplates giving up his role as Batman, but Bruce suggests that Terry find out the truth, leading Terry to confront the elderly Amanda Waller. 

Terry vents some of his frustration about Bruce and his plans to Waller, only to be surprised when Waller reveals that Bruce wasn't responsible for Terry's genetic makeup: she was. Decades earlier, Waller launched a program using her old Project Cadmus connections, codenaming it Project Batman Beyond. Despite the often antagonistic relationship she had with Batman, Waller had surmised Bruce's secret identity, and, as years passed, came to believe that the world would always need a Batman. Retrieving genetic samples from injuries Batman sustained while fighting crime, she obtained the necessary DNA for the next phase of her project.

Tests run found a compatible couple with psychological profiles nearly identical to Thomas and Martha Wayne in Warren and Mary McGinnis. When Warren went in for a flu shot, he was secretly administered a dose of nanites that rewrote the genetic code of his reproductive material into an exact copy of Bruce Wayne's. Thus, Bruce is Terry and Matt's biological father.

Waller hired The Phantasm,  Andrea Beaumont to assassinate Warren and Mary, to simulate the circumstances that propelled Bruce to become Batman. However, Andrea abandoned her mission at the last minute; she told Waller that continuing the Batman legacy by such methods would betray everything Bruce stood for. Waller eventually agreed, and never again tried to have Warren and Mary killed. In spite of this, Warren was murdered years later by Mr. Fixx, the a hit man for Derick Powers, when Warren found out Powers' to sell toxic nerve gas, and Project Batman Beyond ended up succeeding.

Once he leaves Waller's home with this knowledge, Terry comes to terms with the reality that Bruce is technically his biological father, prepares to propose to Dana (who now knows his secret identity), and returns to the role of Batman.

Bruce, being the world's greatest detective, becomes aware that Terry and Matt are his genetic offspring at some point after Terry assumes the role of Batman, and figures out the machinations of Waller and Project Cadmus. However, he never brings it up out of respect for Warren McGinnis, and because he wants Terry to be his own man.