Sly and his crew break into a museum to destroy the Clockwerk parts once and for all, only to find them already gone and the blame put on him by Carmelita. It is found out that a new group of bad guys, called the Klaww Gang, has been stealing the parts, using them for their own personal gain. They track down each member and manage to get back most of the parts, only to have them stolen again and put in the hands of the leader, Arpeggio.
He plans on using Clockwerk to become super strong and eventually immortal. Neyla double crosses him and fuses with Clockwerk to become Clock-La. With the help of Carmelita, Sly defeats Clock-La and its Hate Chip is destroyed, but with the cost of Bentley's legs being crushed. Due to a plea from Sly, Carmelita lets Murray and Bentley go, while he is arrested by Carmelita, although he manages to slip away from her thanks to his friends.