We're all individuals. I might be part of all this, a member of the Cooper line. But in the end... I'm just me. Not Henriette, Thaddeus, Slytunkhamen, Rioichi OR my father... just Sly.
― Sly trying to explain to Dr. M that all Coopers are different[src]
Sly enters the Inner Sanctum and slides down the lasers onto the center platform, admiring the machines made by Thaddeus and others, wondering if they're still operational. Dr. M then enters and claims that they probably are. He then states that he has been looking forward to Sly's death. They fight, Dr. M using his contraption to fly above the lasers. Sly grabs onto legs of his contraption with his cane, all while Dr. M shoots at him. After he lands back on the center platform, he runs to the middle and jumps, hanging from the ceiling, covering himself with a shield. A Cooper boat rises up out of the floor as Dr. M shoots at Sly with a laser. Sly hides under the boat, which is quickly destroyed. Dr. M then drops down, and they engage in battle. Dr. M attacks using water based attacks. Once Sly beats Dr. M, the process repeats with Dr. M flying above the lasers. As Dr. M shoots the laser, Sly hides under a helicopter. They again fight, this time Dr. M using electricity attacks. Again, Sly beats him. After hiding under a third vehicle, this time a car, Dr. M uses fire. Sly defeats Dr. M.
On the brink of defeat, Dr. M. admits that Sly has moxie, and Sly says that he's not sure what happened between him and his father, but that it's not the case with Sly and Bentley. Dr. M begrungingly agrees, noting that Bentley risked his own life to protect him. Sly responds that he would've done the same. Dr. M then says that Sly's father never acted like a friend to him. Sly goes on to say that every Cooper is different, including himself, but Dr. M sees them all the same.
Carmelita Fox then breaks in and claims that both Sly and Dr. M are going to jail. Even though Dr. M admits to defeat, he says that he is going to make Sly suffer, immediately firing at Carmelita. Sly jumps in front of the shot, and is launched into the rafters, passing out. Carmelita says that "no one hurts [her] criminal" and proceeds to attack Dr. M with her shock pistol. She breaks the legs off of Dr. M's contraption, weighing him down with the large tank atop his head. She then jumps up to check on Sly. He awakes and claims to have amnesia, and Carmelita takes advantage of the situation, saying that he is her partner, "Constable Cooper." Sly says that they had better get out of there, that the ceiling is going to fall down. Bentley then jumps through the door, entering the Inner Sanctum, calling for Sly. The mission then ends.
- When Sly is talking about his ancestors, the subtitles misspell "Thaddeus" as "Thadius."
- This is the only final job in Sly 3 not to have "Operation" in the title.