Two years after defeating Clockwerk, Sly Cooper breaks into the Museum of Natural History in Cairo to steal the Clockwerk parts and destroy them to end his threat against Sly's family for good, but discovers that the parts are already missing. Inspector Carmelita Montoya Fox and her new partner, Constable Neyla, confront Sly, but he escapes before Carmelita and Neyla can arrest him. Before making his escape, Sly hears Neyla suggest that the evidence actually suggests that the Klaww Gang stole the parts for their own use.
The Cooper Gang heads to Paris, where the first Klaww Gang member Dimitri is using Clockwerk tail feathers as printing plates to create counterfeit money. Sly and the gang shut the operation down and Dimitri is arrested by Interpol. The gang then heads to India, where the second Klaww Gang member Rajan puts Clockwerk's wings on display at a ball he is hosting. Rajan is also the kingpin of a local crime syndicate that grows and sells "spice", an illegal plant indigenous to the Indian jungle. Also present at the ball are the other Klaww Gang members and several undercover Interpol agents, including Carmelita and Neyla. The gang steals the Clockwerk wings in the middle of the ballroom while a disguised Sly creates a distraction by dancing with Carmelita. After the Cooper gang escapes with the Clockwerk wings, Carmelita blows her cover and starts making arrests. The Klaww Gang flees the scene, and Rajan goes into hiding somewhere deep in the jungle. The gang tracks him to his spice-growing facility in a long-abandoned temple, where he is using half of Clockwerk heart to super-irrigate his spice crops. He carries the other half of the heart on the end of a staff that he carries with him at all times. The gang steals both halves of the heart and incapacitates Rajan, but Carmelita, Neyla and the Contessa arrive. Neyla frames Carmelita of working with the Cooper Gang on the night the Clockwerk wings were stolen. She betrays the Cooper Gang and puts Sly, Murray, and Carmelita under arrest.
