Plot

Two years after defeating Clockwerk, Sly Cooper and his band of thieves must recover and destroy all of the stolen Clockwerk parts from a sinister organization before their old nemesis can return from the dead.

Two years after Sly Cooper had destroyed Clockwerk, the leader of the Fiendish Five, he brought his good friends Bentley and Murray to Cairo, Egypt to secure the parts of Clockwerk from getting stolen. However, the parts were already taken by a spice organization called the Klaww Gang.

Sly and his friends arrived at Paris to get Clockwerk's tail feathers from spice dealer and art forger Dimitri Lousteau. With the tail feathers, Dimitri was able to print unlimited forged money. Sly was able to get the tail feathers and let Carmelita Fox arrest the lounge lizard.

The gang's next heist was at a ballroom in India, owned by a spice lord named Rajan. He used Clockwerk's wings at a statue within a ball. There, Sly encountered the other members of the Klaww Gang and two other cops; Constable Neyla and the Contessa. After getting the wings, Rajan fled to an ancient spice temple so he can create more spice with Clockwerk's heart. The gang did get Clockwerk's heart but Bentley was left behind as the Contessa took Sly and Murray.

Bentley learned that the Contessa is part of the Klaww Gang and sent Sly and Murray to a prison at Prague. Bentley helped free Sly and Murray before they moved to a haunted castle estate. There, the Contessa used Clockwerk's eyes to hypnotize people more easily. It became a war between Neyla and the Contessa. Sly managed to take both of Clockwerk's eyes as the Contessa was sent to prison.

Sly and his friends followed a trail of spice shipments to Canada, home of Jean Bison, a preserved bison from the 1850s, who owned Clockwerk's lungs and stomach to operate his three trains. Bison later moved to a lumber camp where he clear-cutted trees with Clockwerk's talons. Bison was ready to get picked up by Arpeggio, the leader of the Klaww Gang. He told Bentley that he sold all of the Clockwerk parts to Arpeggio. After the confrontation, Sly and his friends got stuck in a battery sent to Arpeggio's blimp.

Arpeggio used Clockwerk's parts to become immortal, but Neyla (the true villain) went inside Clockwerk to become Clock-La. Clock-La was driven by hate as she set foot on Paris. She crippled Bentley until the Hate Chip was destroyed. Murray blamed himself for crippling Bentley as Sly had a brief talk with Carmelita.