El Jefe has played dictator for the last time and it is time for the gang to put an end to his schemes.
The Cooper Gang is ready for the final operation to take down El Jefe. The first step is getting the gate open. Since the guards are already knocked out, Sly can open without getting detected. On both sides of the gate are two dragon mouths that shoot fireballs. Sly uses his Samurai Costume to reflect the fireballs back into the mouths, which in turn opens the locks on the gate.
The rest of the team, along with Rioichi, shows up and they head through the gate and up the stairs leading to El Jefe's fortress. When they get in view of El Jefe's fortress, a big, giant blimp appears from below and rises into the sky. The gang runs forward to get into the fort, but runs into El Jefe on the bridge. He has the rat troopers deal with the gang while he heads through the door. The gang defeats the guards on the bridge, while Rioichi heads down below to make his way to the machine wheel to open the door. Once done, he climbs back up to the top, by which point all of the guards have been beaten.
The team presses on and El Jefe appears again, pouncing on Rioichi and steals his cane to deliver it to a new owner. He then runs across the bridge, scraping the surface with his katanas and causing it burn up and fall apart. Sly tells everyone else to stay there, while he presses on to get Rioichi's cane back. He hops across the destroyed bridge and makes his way to El Jefe's throne room. He taunts Sly and then lifts off using a rope.
Sly then climbs up to the highest part of the structure. El Jefe, wielding two swords with electric and fire abilities, battles Sly throughout this area. Sly jumps over the electric attacks, but uses his Samurai Costume to dodge the fire attacks.
After three rounds, Sly beats El Jefe. Once he falls, Sly proceeds to grab Rioichi's cane, but a small tin of gas falls by his foot and as hears the timer, he jumps off of the edge and hangs off of it. Two rat troopers drop down from the blimp. One of them grabs Rioichi's cane from El Jefe's unconscious body before they are lifted back into the blimp. Sly catches a glimpse of a silhouette of someone watching from the window. As the rat troopers ascend, one of them unknowingly drops a sheriff's badge, which rolls up to Sly. The blimp then disappears in a flash, leaving Sly stunned. At this point, the operation is over.
- The area where you fight El Jefe is not seen in the Feudal Japan hub.
- This is the last time we see Murray in his Geisha Costume, then it is never seen again.
- This is the first heist that does not have "Operation:" in its title.