Cooper! You will never be rid of me! Clockwerk is superior!
― Clockwerk's final words[src]
After recovering Carmelita's jetpack, Sly confronted Clockwerk directly above his sunken death ray. The owl recognized Sly's efforts as being remarkable and stated that the Coopers "always" found a way to beat him. Sly then inquired about his age, and the mechanical beast arrogantly replied that "perfection has no age" and explained that his hatred for the Cooper Clan allowed him to live for thousands of years.
Shortly before the battle began, Carmelita warned Sly that her missiles would not hurt Clockwerk but would create holes in his armor, thereby ordering him to shoot into the gaps she created.[note 1] With Carmelita providing distant assistance, Sly used the jetpack to maneuver himself around Clockwerk's attacks and shoot the owl at his most vulnerable spots. He eventually caused enough damage to the owl that caused him to become weakened and fall into the lava below.
As soon as he was assumed to be defeated, Clockwerk resurfaced, and Sly inquired about why he spared Sly's life when he and the Fiendish Five stole the Thievius Raccoonus. Clockwerk explained that he wanted to show the world that the Cooper line was nothing without the Thievius Raccoonus. Sly pointed out his flaw, stating that the Thievius Raccoonus is a product of great thieves, not the other way around, a sentiment that angered Clockwerk. After a second battle, Clockwerk fell once more, but this time he was severely damaged. Sly seized control of the jetpack and dropped down to finish Clockwerk off face to face before his auto-reconstruct circuitry kicked in. In Clockwerk's final moments, he told Sly that he would never be rid of him and that he was superior. As he shared these last words, Sly hit his damaged head with his cane, decapitating him and ending the Clockwerk menace.
As Sly stood on the catwalk overlooking Clockwerk's lair, he was proud to have fulfilled his goal of defeating the Fiendish Five and reclaiming his family's birthright. He acknowledged his two friends for their efforts and sticking beside him throughout the entire journey. Unfortunately, this victory also meant that Sly's partnership with Carmelita was over, and they were back to playing cops and robbers. Though Sly was sure Carmelita was going to arrest Sly right away, she kept her word and gave Sly his ten-second head start. This gave Sly plenty of time to first kiss Carmelita and handcuff her to the catwalk. Sly and his gang made their escape out of the Krakarov Volcano, and though Sly felt bad leaving Carmelita stranded on that giant rock, he knew their paths would cross again soon.
- Despite Carmelita saying that blasts from her shock pistol cannot harm Clockwerk, they actually deal a little bit of damage to Clockwerk. It is possible to complete the first two parts of the battle without shooting Clockwerk, though this would take a very long time.