On a boat ride with Lupin, Fujiko causes an accident with another boat. Lupin swims over to the boat's remains to make sure that the rider is okay and discovers an enchanting girl named Linda. Fujiko, meanwhile, steals Lupin's boat, stranding him. A huge ship armed with gunmen appears and attempts to shoot at Lupin and Linda, but a shot from Jigen takes out the primary assassin and causes the boat to steer away, saving them. When Jigen meets up with Lupin, Linda has disappeared.
Jigen's research shows that the woman was the assistant of Doctor Highline on the island they are at. Lupin and Jigen get on diving gear and attempt to infiltrate the underwater base of criminal organization Killer in Killers who also are stationed there. The two are instantly detected by the organization's radar and are shot at, prompting a quick escape. They get ashore and camp in the wilderness of the island. Jigen wonders why it was easier to infiltrate the organization compared to their previous try.
Suddenly Lupin smells something, which he recognizes as the scent of Linda. Instead, it's actually a field of flowers that the scent is coming from. Linda appears, and Lupin follows her in a game of tag.
After the romp with Linda in the flowers, Lupin and Jigen meet Doctor Highline, who has been forced to experiment with the Third Sun flowers that grow exclusively on the island for the benefit of Killer in Killers. The flower's extracts can be used to create powerful explosives. He tells them that his inhumane experiments with his secretary Linda in the past caused her to become a witch whose life depends on the flowers' well-being themselves.
Meanwhile, Fujiko is attempting to take the flowers for her own benefit, and meets with Linda who has told her about the flower bed. Killer in Killers' leader watches them from afar, knowing exactly what is going on. Fujiko tries to take some of the flowers away by plane, but the organization shoots it down with missiles, its leader stating that the flowers aren't allowed to leave the island. Lupin and Jigen track the plane down and discover Fujiko, who explains that she pretended to work with Killer in Killers. Then they're ambushed by the leader of the group and Lupin is captured.
Inside the base, the leader introduces himself as Starn. He explains that he wants Lupin to work with them and retrieve a missile containing Third Sun products from the ocean where the organization accidentally lost it. Lupin declines and then switches places with Starn, exiting the prison cell in disguise. Despite this, his trick is quickly discovered and he has to dodge gunfire while escaping. Jigen shows up and rescues Lupin from more armed guards and the two get in Doctor Highline's car.
Later, Starn is overseeing the bulldozing of the Third Sun flower beds when a plane shows up, dousing the fields in gasoline. Lupin lights the fire, but they've left Linda on the ground in the middle of the fire. Linda fears that her life is ending because the flowers are dying. Doctor Highline retrieves his gun and shoots Linda, who magically disappears into nothing.
With the Third Sun flowers gone, there's one last thing to take care of. Lupin dives into the water and discovers the submarine housing the Third Sun missile. Starn follows Lupin and tries to take back the missile, but Lupin says that Highline wanted the missile to go to a Japanese research laboratory. Starn gets knocked out by Fujiko, who tells Lupin that the missile can only reach Japan if one person is piloting it. Lupin, disappointed, goes in alone and launches the missile. Suddenly Fujiko shows up from behind and because of the weight, the missile crashes back into the ocean. They salvage the parts and end up going back to Japan via rafts. Jigen scolds Lupin for working with Fujiko again while she tans herself in the sun.
- MacGuffin: The Third Sun flowers.
- Mercy Kill: Doctor Highline shoots Linda before she can be extinguished by the fire and the flowers' death.