Oh boy. Here comes the big guns... and by "guns" I mean a giant flying whale-dragonfly thing covered in robotic junk! Wait! Dr. M is plugged into that monstrosity!
The air defenses covering Kaine Island need to be destroyed so that the Cooper Gang can gain access to the Cooper Vault. Sly decides that he is done sitting out missions after being attacked by the Mutant Primate and that he will fly the Biplane.
Sly takes out the sensor banks for the fourteen missile defense turrets, which don't have a guiding system thanks to the previous work by Penelope. After the last turret's sensor bank is destroyed, fighters fly up from out of the ocean. Sly destroys them as well, by first disabling their shields with a well-placed missile, then shooting them out of the air. After all twenty fighters go down, the Whale-Fly emerges from the sea, with Dr. M plugged into it. He expresses joy in the fact that Sly is flying, and wants to show that he is the master of the sky, no longer second-fiddle.
Sly shoots at the shield that covers Dr. M, and Dr. M retaliates with releasing missile pods and other defense systems. After Sly does as much damage as he can to the Whale-Fly, Dr. M laughs at him, saying that the guns are nothing more than toys to his creations. Sly jumps from the biplane and paraglides onto the Whale-Fly, despite Bentley's disapproval.
After landing on it, Dr. M reveals that both he and Jim McSweeney belonged to his father's gang, and that he was as self-centered as Sly, who named the Cooper Gang after himself. Sly attacks Dr. M and steals his cane back, knocking Dr. M into the ocean in the process, then jumps off the Whale-Fly, gliding over to the entrance of the Vault. He opens it, then contacts Bentley, expressing his want for him and Murray to be with him as he enters the Vault. The Panda King fits the Cooper Van with rockets that launch it up to the entrance. Murray drives the Van inside, and Sly follows. Mission complete.