I had two ideas.
One has Will being part of a villain project to clone and replace several heroes. The League and the government shut it down but Jim Harper adopts him and passes him off as Roy's cousin.
The other has Will created by Vandal Savage as a back up body and having enhanced physiology. When he starts showing signs of independence, Savage tries to kill him but he is rescued by Scandal Savage and secreted away to live a life free from Savage until he and Roy cross paths one day.