Lupin, Goemon, and Jigen board a mini-helicopter and fly to the enigmatic "Drifting Island" in search of a treasure claimed to be concealed somewhere on the island. The group comes into the dangerous "Nanomachine," the island's security system, while exploring the island. The trio sets off the alarm, causing "the Nanomachine" to come to life. The little nation of Zufu holds the key to uncovering the island's enigma. The vicious, knife-collecting General Headhunter now rules this once-prosperous nation. Fujiko does her normal investigation and hacks into General Headhunter's computer in the hopes of discovering vital information. Lupin has sent Zenigata a video message in which he expresses his yearning for the rare gem. Oleander, a fiery blond cop with her own dark secrets, steps in to help Zenigata. Armed with their newly found information, Lupin, Goemon, Jigen, and Fujiko go back to “Drifting Island,” but this time they are followed by General Headhunter.