Willy only appeared twice in the Batman Beyond series. The first was when he was using the Golem as a way to get revenge on those who picked on him. He was defeated by Terry McGinnis(Batman) and the Golem was destroyed. He went to juvenal and was not seen again until his second and final appearance. His second appearance showed that the his powers had evolved to show that he now had psychic powers. He had also gotten his body into shape so now he had the body of a musclebuilder.
A few weeks after Willie's attempt on Nelson's life, Sam Bifford, a former con, designed neural headgear and a toy for his autistic son Morgan. The supplies that Sam used to make the headgear and the toy came from the scrap heap where Sam worked. However, the supplies derived from the original Golem and WIllie's headpiece which he originally used to control the Golem. Sam intended for the toy to act as Morgan's avatar in order to express Morgan's emotions as well as his actions.
After leaving the McGinnis home, Sam is approached by child services as well as the police. It seems the scrap heap company that Sam works for, was commissioned to destroy the remaining pieces of the Golem after its destruction but they failed to do so. When the company learned that Sam had collected pieces of the Golem to make Morgan's toy, they decided to use him as a scapegoat for the theft of highly sensitive industrial prototypes that were paid to be destroyed. Sam's arrest causes Morgan to become angry and Morgan's rage makes the Golem toy sentient as if it were Morgan's own avenger.
Sam calls the McGinnis family for help and Terry has Bruce bail Sam out of prison. Bruce informs Sam that he will have his lawyer defend him during the proceedings but he advises Sam to keep away from Morgan for the time being since child services has issued a restraining order against Mr. Bifford. Terry heads to the junkyard where Sam works at, to find clues for Sam's defense. Terry scours through the junk and finds pieces of the original Golem. Just as Terry reports his find to Bruce by via comm link, he comes under attack by the Golem toy. However, the toy has grown in size because it has been collecting contraband junk that the company was also commissioned to destroy but never did. The Golem remembers Terry as the Batman, when he defeated Willie Watt at the school prom. The Golem unleashes an arsenal of weapons on Terry before it makes its quick escape and leaves Terry unconscious.
After Terry's run in with the new Golem, Terry figures Willie Watt is probably behind this so he heads to the isolation cell block at juvie hall where Willie is being kept under observation. Terry asks Willie if he is behind the ressurection of the Golem. Willie says he isn't but he was overjoyed to hear Golem's sudden return. Willie tells Terry that someone else with an unusual kinetic ability has awoken Golem and the Golem will do anything to protect his new keeper. On the other side of Gotham, Sam visits Morgan at the Tim Dini Foster Center for Boys. Morgan sat on the other side of the center's playground while the other children played.
Sam tries to comfort Morgan but the police arrive to arrest Sam because the lady in charge of the center had called them. This act angers Morgan even further and suddenly, the Golem appears. As Morgan screams for his dad, the Golem begins to scream for Sam as well. Terry now knows that Morgan was the unintentional user of the Golem. The Golem frees Sam from police custody and Terry grabs Morgan to reunite him with his father. With father and son together again, the Golem ceases to move because it knows Morgan is safe.
Unfortunately, the police used a grenade launcher to destroy Golem before it could do anymore damage. Afterwards, Sam was cleared of all charges, the company was held liable for their failure to destroy highly dangerous materials and Sam was compensated for the anguish that the company brought him as well as his son. As for the Golem, its cpu was saved and placed in Morgan's new toy.