The Clockwerk parts weren't destroyed and were recovered by Interpol, eventually being put on display at a museum in Cairo, Egypt. It was here that some new organization known as the Klaww Gang stole the parts before Sly and his team managed to do so. The Klaww Gang used these parts to do crimes and they eventually found their way into the hands of Arpeggio.
Arpeggio reconstructed Clockwerk and had plans to merge with it to become immortal. However, he was betrayed by Constable Neyla who ended up fusing with Clockwerk to become Clock-La. Clock-La captures Bentley and Murray, and with the help of Carmelita Fox, Sly manages to defeat it and rescue his friends. They discovered that the power of Clockwerk comes from the Hate Chip, so Bentley and Murray manage to get a hold of it, although Bentley is injured in the process. Carmelita destroyed the Hate Chip, which made the Clockwerk parts deteriorate right then and there, putting an end to his legacy.