Future Boy Conan

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.

As new earthquakes begin to herald Industria's incoming destruction, Lepka, who has survived the crash of his flyer, and a troop of loyalists secretly channel some solar power underground to charge up the Giganto, a giant warplane left over from the last war. When the power leak is discovered and cut, Lepka's forces covertly seize the control room and continue to divert power to the plane. Noticing the takeover, Lana and Monsley escape aboard the Falco to inform the others. Conan and his friends have just finished raising the sunken passenger ship when Lana and Monsley warn them about Lepka, and they return to Industria; but having completed recharging, the Giganto takes off. Conan's group attempts to stop it, but ends up crashing through the plane's surface. After pushing the Falco back out to enable Monsley and Lana to return to Industria, Conan, Jimsy and Dyce infiltrate the Giganto.

Conan descends to the residential area to rescue Lana. After overhearing Lepka's intentions to flood the caverns, he attempts to defuse the bombs used to create the flooding breach, but is unsuccessful. Lana gives herself up to save the residents; but after she is back in his hands, Lepka seals the exit anyway, leaving the people to drown. When he takes Lana to her grandfather, however, he is forced to learn that Dr. Lao has gone numb and blind from his tortures, rendering further threats against him useless, so he tries to force Lana to contact him by threatening to plunge her off the Triangle Tower. In the meantime Conan rejoins Dyce and Jimsy, and they exit the caverns through a flooded earthquake fissure, where they rescue Monsley, who was about to be executed. They manage to open the main shutter to the caverns, and the residents storm the Triangle Tower.

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.

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.

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, 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.

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.

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 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.

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.

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 Lana is kidnapped by the two soldiers from Industria, Conan fails to rescue her. Conan's grandfather dies from his injuries. After burying his grandfather, Conan builds a boat and sets off to rescue Lana.