Bentley: Breaker Alpha Foxtrot, this is the Wizard, do you read me, Sitting Duck?
Sly Cooper: This is Peking Duck, I hear you, Blizzard.
― The two addressing each other by their codenames[src]
Two years after Clockwerk's defeat, the individual pieces of his body were placed on display in the Museum of Natural History in Cairo, Egypt. Fearing that the mechanical owl could be resurrected if the parts fell into the wrong hands, the Cooper Gang needed to get to them before anyone else and destroy them.
Sly, Bentley and Murray ran across some rooftops and parted ways to take up their positions in the museum. Once Sly slipped down into the main exhibit, he pulled out his binocucom and reviewed the mission with Bentley. They first attempted to address each other by their codenames, but since Sly kept failing to get Bentley's name right, the two resorted to plain talk. When Sly asked for Bentley's status on the heist, the latter explained that he was stuck in the basement and needed Sly to activate the elevator for him.
By climbing onto a whale skeleton that hung from the ceiling, Sly was able to reach the upper floor, where he flipped on the elevator switch. Once Bentley exited the elevator, he approached the nearby computer and began hacking into the museum's security system, shutting down the security in the next set of halls and opening the large security gate beside them. Sly commended Bentley on his efforts, given this was the latter's first time out in the field. However, the operation was far from complete. Bentley decided to stay behind and provide computer support, while Sly went on to meet up with Murray at their rendezvous point. To avoid raising suspicion of the security shutdown, Bentley disguised his voice to impersonate the network administrator and addressed the security guards about some new software being installed into the security mainframe.
Once Sly approached a balcony, Bentley contacted him again to direct him to one of the buildings across from his position, which held the Clockwerk parts. He also reminded him that he would need to meet up with Murray. Since the route through the garden below was heavily guarded, Sly decided to take the long way around, by using his Raccoon Rail Walk to traverse the tightropes that would get him to that building.
I don't get it, Sly. The Clockwerk parts should be here. This is all wrong! We need to pull the plug on this operation right now!
He soon reached the balcony of said building, but Bentley suggested he try and press on without Murray since he was nowhere in sight. However, after a brief moment, Murray dropped down from above, breaking through the skylight. Sly stood a safe distance from the impact of Murray's new move, the Thunder Flop, a move that knows neither friend nor foe, only destruction. "The Murray" then offered his assistance by opening the security gate. Once the two approached another balcony, Murray hurled a statue towards the gate that blocked access to the Clockwerk exhibit. The rope that connected from this balcony to that building would not hold Murray's weight, leaving Sly to press on by himself, though Murray promised to wait in the hallway to help with carrying out Clockwerk's parts.
Upon entering the exhibit, however, Sly found the room empty. Knowing that something was wrong, Bentley insisted they call off the mission right away. Sly was then busted by Inspector Carmelita Fox and her partner, Constable Neyla, who appeared out of two sarcophagi against the far wall. Carmelita ordered Sly to freeze before accusing him of stealing Clockwerk, leaving him to realize the parts have already been stolen before they did. Neyla pointed out, however, that the Klaww Gang may have been responsible for the theft, given the method of entry and guard casualties.
With the two officers briefly distracted with their conversation, Sly took this as an opportunity to sneak away. Carmelita soon took notice and gave chase, without Neyla joining her. Sly led the chase through a long exhibit hall and was soon accompanied by Bentley and Murray. Upon nearing the end, the gang decided to part ways, that way Sly could keep Carmelita distracted while Bentley and Murray get the team van started. Upon reaching the end of the hall, Sly busted through a window and led the chase along the rooftops while the team van was being pursued by police cars below. Sly then slid down to the street below, and the van pulled up just in time for him to jump in through the back. Once Sly was inside, the gang drove off, narrowly missing the fleet of police cars and leaving Carmelita just as furious as ever.