Jimsy and Conan sneak onto the ship, but Jimsy gets drunk and alerts the captain of their presence. After the boys are caught, Captain Dice lets Conan and Jimsy stay on the ship if they will take punishment. Jimsy passes out and Conan takes both their beatings. They work on the ship doing random jobs. Finally, the ship sets sail for Industria.

After the Barracuda arrives in Industria, Conan is thrown in the brig after he assaults Monsley who was visiting the ship. Lepka, the self-serving chief administrator of Industria's High Committee, tries to threaten Lana into telling him where her grandfather is. Monsley decides to take Conan in for "re-education". When the soldiers come to take him, Conan escapes and, after a rough flight through the bowels of Industria, eventually finds Lana.

While making their escape, Conan and Lana come upon a plane from the last war that Lepka wants to power with Dr. Lao's solar energy process for his plans of world conquest. They are captured, and Lepka threatens to hurt Conan if Lana doesn't tell him where her grandfather is, but she refuses. Upon witnessing Lepka's viciousness, Dyce decides to help Lana. Dyce and his crew kidnap Lana and make their escape on the Barracuda.

Dyce escapes in the fog. Lepka gets permission to use the gunboat and Falco to pursue Dyce. Conan escapes from jail and sneaks onto the Falco. Jimsy informs Lana that he is a companion of Conan. Dyce meets with Lana and when she gets angry that he left Conan he opens the window and threatens to throw her out. The Falco sees the light and follows the Barracuda. Conan escapes and attempts to board the Barracuda.

Lana escapes and uses a lifeboat to save Conan. The gunboat boards the Barracuda and captures Dyce and his crew. Lana and Conan escape on the lifeboat. While trying to make it to the shore, the gunboat blows up the lifeboat, but Conan and Lana survive and make it to the nearby island, where they discover an old battlefield littered with tanks. Lana hears her grandfather by telepathy, and Conan and Lana set out to cross the desert.

After crossing the desert, Lana and Conan are discovered by a man named Patch, who works at an Industrian salvage platform where a passenger ship is about to be uplifted from the seabed. After proving his diving skills to Patch, Conan and Lana are set to work. Terit, an ambitious worker on the platform who longs to be elevated to a higher grade of citizenship in Industria, tries to identify them. He sneaks onto the Falco, which stopped by, and informs Monsley that Conan and Lana are there.

Terit returns to Industria and is given a radio to inform Lepka when Lana meets her grandfather. However, an earthquake hits the desert island; Patch goes down and gets trapped beneath the ship, and Conan rescues him. When Patch is revealed to be Dr. Lao, Terit informs Industria of Dr. Lao's presence; but another tremor causes the beach near the salvaging platform to sink into the ocean, and the platform begins to float out to sea. Knowing that Industria will send forces to capture them, Lao, Conan, and Lana escape in a small lifeboat.

Lana and Lao descend to the Triangle Tower's Core Block to acquire the IC chip they need to repair their flyer. While Dyce and his crew - minus Jimsy, who refuses to abandon Conan - turn tail, Conan frees some prisoners who have rebelled against Lepka, and together they search for Lao. Luke, the leader of the prisoners, leads Conan and Jimsy to the Core Block, but Lepka and his soldiers arrive there as well. With the help of the ex-prisoners, Conan's group escapes the Core Block and heads to High Harbor, with Dyce and his crew joining them along the way.

Lao drops the children off on the Baracuda and heads back to Industria in order to aid its citizens against the impending cataclysm. The Barracuda proceeds to High Harbor, where the local residents initially meet the ship with hostility until Lana is able to explain that the crew has joined their side now. While the Barracuda crew is allowed to disembark from their damaged ship, Lana gives Conan and Jimsy a tour of the island, thereby encountering Orlo, the overjoyous villagers and Lana's aunt and uncle. After hearing her story, Conan and Jimsy are allowed to stay.

Conan, Jimsy, and Lana go to Windmill Village, High Harbor's industrial district. After taking a brief tour, Conan and Jimsy decide they will go fishing and hunting to earn their daily bread. While fishing, Conan meets Mr. Gull, who takes care of the village fish preserve, and begins working for him. Jimsy meanwhile is chased by and kills a massive wild boar when they both fall over the edge of a cliff. He butchers and cooks the pig, and brings it back to the village for the people to eat. The victory is short-lived, however, since the pig was not wild but belonged to Orlo. After learning of this, Conan and Jimsy go to Orlo to take responsibility.

As they reach the mountain, Conan and Jimsy are attacked and captured by Orlo's anarchist gang. They make a deal that Orlo will forget about his lost pig, if they can prove that they really brought it down by defeating another one of his boars. Using cleverness and teamwork, they succeed, and Jimsy decides to work for Orlo; but when Oslo's sister Tera tries to steal a goat from Tito, a herder from another village on the other side of the island, Jimsy quits. Just as matters begin to get ugly, Lana, who has noticed Conan and Jimsy's absence, arrives and gives a memento of her mother, a valuable necklace, to compensate for the lost pig.

Lana has a premonition about an Industrian attack on High Harbor, a message she is sure was sent by her grandfather. To ease her mind, Conan takes her to Tito's village, where Jimsy has become a pig herder, and he also shows her the treehouse they have erected to live in. Meanwhile, Orlo is visited by Dyce, who has tired of life on land and wants to set out to sea again. Dyce convinces Orlo to help fix the Barracuda, in return for Dyce helping to kill Conan and Jimsy. But at the very moment the deed is to be committed, Industrian troops under Monsley launch an attack against High Harbor.

Conan and Jimsy, who have escaped Orlo's attempt on their lives, scout out the Industrian ship, while Lana warns the village about the incursion. Orlo's men try to fight the invaders but are defeated. After rescuing Tera, Conan, Jimsy and Dyce hurry to the village to help the villagers organize their defense. By landing on the wrong side of the island, Monsley has lost the element of surprise, but Orlo and his men switch sides for Industria, infiltrate High Harbor's defenses and betray them from within. Lana is knocked out by a cannon blast, and when Conan sees Jimsy's pet piglet, which was entrusted to Lana, arrive on its own, he immediately rushes to save her.

Conan saves Lana from Industria's soldiers but gets knocked out; Lana manages to hide him before she gets captured and taken aboard the gunboat. Industria occupies High Harbor, and Orlo is installed as a puppet governor. To deprive them of their only means of support, Conan and Gil, the only villager to escape, prepare to sink the gunboat with explosives. But after planting the charge, Conan learns that Lana is aboard and boards the vessel to retrieve her, but ends up captured. After tricking the crew into taking him out of his cell, the charge detonates, sinking the ship and allowing Conan to rescue Lana from her cell.

The village chief lets the soldiers join their community. Conan decides to return to Industria using an old seaplane left by Dr. Lao in the fish preserve cave. Together with Jimsy, Monsley, Lana as a last-minute joiner, and Dyce as a stowaway, Conan departs High Harbor; but just upon reaching Industria, the group encounters the restored Falcon. After letting Lana, Dyce, and Jimsy disembark, Conan and Monsley distract the Falcon by leading it away from their friends.

Evading Lepka's attempts to eliminate them, Conan, Jimsy, and Dyce start inflicting critical damage to the Giganto. While Dyce and Jimsy eventually end up getting jettisoned inside the tail rudder, Conan confronts Lepka as he tries to get away in an escape pod. Despite Conan's attempt to save them, Lepka and the rest of his men are left to perish aboard the doomed Giganto. A week later, as the final stage of the cataclysm arrives, all the Industrians except the High Council mount the restored passenger ship and watch Industria sink into the sea.

On its way to High Harbor, the passenger ship recovers Conan, Dyce and Jimsy from the sea; and after asking Conan to look after Lana, Dr. Lao dies contently. Sometime later, the old and new inhabitants of High Harbor conduct a double celebration surrounding Dyce and Monsley's wedding and the relaunch of the Barracuda. Many of the new settlers, including Conan, Lana, Jimsy, Tera, Luke, Monsley and the Barracuda's crew, leave to establish a new colony on Remnant Island, now expanded by the cataclysm into a new continent.