July, 2008 A.D. Mankind was facing the fires of annihilation. Super electromagnetic weapons, far more destructive than atomic weapons, caused half the world to be wiped out in an instant. The Earth was seized by great tectonic upheavals. Its axis was tilted. The five continents were ripped completely apart and sank into the sea.
Conan met another boy Jimsy who became Conan's friend and joined him in his journey to Industria. Conan and Jimsy sneaked on board the Industrian ship Barracuda but they were discovered and enslaved by Captain Dyce. Soon after arriving at the port of Industria, Conan was imprisoned for trying to attack Monsley. With the help of Jimsy, Conan got away and rescued Lana from the Triangle Tower, where she was imprisoned. Pursued by Industrians, Conan and Lana entered a huge underground shelter where they discovered Giganto, the last of the giant moth-like planes that were used to destroy much of the world during the war. Eventually they were captured by Lepka, the administrative head of Industria. Meanwhile Dyce was angry after being reprimanded by Lepka and the Industrian High Council for his ineffectiveness in capturing Lana. Dyce and his men overcame the guards and coerced Lana to follow them to the Barracuda. With Lana on board, the Barracuda set sail for High Harbor, Lana's home town. Conan freed himself from jail and sneaked onboard the hydroplane Falco sent to intercept the Barracuda. The Industrian Gun Boat was also sent after the Barracuda.
While the Barracuda was under attack from the Gun Boat, Conan and Lana escaped using a small speedboat. Though the speedboat was eventually destroyed, Conan and Lana managed to swim ashore and ended up on the edge of a vast wasteland. Apparently guided by Dr. Lao through telepathy, they barely made it through the desert and were picked up by Patch, an unfriendly-looking one-eyed Industrian who oversaw the salvage operation of a sunken Industrian ship. Conan and Lana were forced to work on the salvage ship and they were treated rather roughly by Patch, who however was also secretly protecting them... Patch's true identity was revealed when he had to call for Lana's help using telepathy while he was trapped underwater - Patch was none other than the elusive Dr. Lao. Having revealed his identity, Lao fled with Conan and Lana. He had hidden a flying machine in the desert but it was in need of repair. Since the necessary parts can only be found in Industria, they returned to Industria using the half-crippled flying machine.
Alerted by a tip from Monsley, Lepka tried to trap Lao in the underground chambers of the Triangle Tower, but Conan and Jimsy managed to save Lao. With the help of the underground residents, they escaped from the Triangle Tower and caught up with the Barracuda. Instead of returning to High Harbor with the others, Lao decided to go back to Industria so that he could warn the Industrians of the impending geological disaster he had predicted on the basis of seismic observations.
Upon entering High Harbor, the Barracuda was ambushed by fishermen who recognised it as the ship that took Lana away. The Barracuda was rather badly damaged and was beached in the harbor. Lana, Conan and Jimsy were greeted warmly by the villagers who rejoiced at Lana's safe return. Conan and Jimsy were treated like heroes and they enjoyed the hospitality of High Harbor. One day Jimsy went hunting in the wrong territory and killed a wild pig that belonged to Orlo, the leader of an anarchist gang of orphans who lived on the other side of the mountain. When Orlo tried to gain advantage of the villagers using the incidence, Conan and Jimsy went to negotiate with Orlo. Jimsy met Tara, Orlo's little sister, and he was tempted to join Orlo's gang. Eventually he changed his mind which made Orlo angry. Orlo enlisted the help of Dyce and tried to kill Conan and Jimsy. But before they can accomplish that, the Industrian Gun Boat appeared outside High Harbor and an invasion party disembarked ...
Orlo organized his gang to fight the Industrian soldiers who landed on his side of the territory by mistake. Fierce though Orlo's gang was, they were no match for the guns and cannons of Industria. Orlo and others were captured but Tara was saved by Conan and Jimsy. Orlo offered to help Monsley invade High Harbor in return for his appointment as local leader under Industrian rule. Monsley agreed and Orlo tricked the villagers into surrender. Lana was captured and imprisoned aboard the Gun Boat. Conan and a few others fought the occupying Industrians with guerilla warfare. By sneaking a large bomb onboard the Gun Boat, Conan managed to sink it and rescued Lana. Monsley didn't want to admit defeat and tried to order the villagers to repair the beached Barracuda. Her plan was spoiled when a hugh tsunami hit High Harbor and carried the Barracuda half way up a hill. Realizing there's no way to win, Industrian soldiers gave up their arms and surrendered. The soldiers were allowed to join the villagers as members of High Harbor but Monsley had difficulty fitting in. Meanwhile Conan decided to go back to Industria to try and help Dr. Lao. Jimsy was reluctant but agreed to follow Conan. But with both the Gun Boat and the Barracuda gone, the only means of returning to Industria left was an advanced seaplane used by Lao years ago when he rescued people from Industria. However, Monsley was the only person in High Harbor qualified to fly the seaplane, and so Conan asked for Monsley's help. Monsley was shocked by Conan's seemingly naive suggestion but had no reason to refuse. Lana wanted to go with them but Conan asked her to stay behind because of the danger. But at the last minute Conan realized how much Dr. Lao meant to Lana and he took Lana with him. Dyce also managed to sneak onboard.
Half way to Industria they spotted the Falco and tried to outrun it, with apparent success... With Industria in sight, Monsley suggested to Conan that they went their separate ways after landing. She was surprised when Conan didn't object and said he'd agree if that's what she wanted. Moved by Conan's unquestioned trust in her, Monsley decided to follow Conan instead.
No sooner had the seaplane landed on Industria than Falco appeared again and opened fire. Lana, Jimsy and Dyce stayed ashore while Monsley and Conan tried to lure the Falco away with the seaplane. The seaplane was hit and went down near the Triangle Tower. Conan was captured when he tried to rescue the unconscious Monsley from the burning seaplane. Lana and others slipped into the underground in search of Dr. Lao, hoping that he might help rescue Conan. Unfortunately Lao had already been captured and was being tortured constantly by Lepka. However, Lao refused to reveal the secret of solar energy unless Lepka agreed to use the solar power only to help Industrians escape from the impending geological cataclysm. Lepka wouldn't agree since he wanted to use the solar energy to revive Giganto so that he can rule the world. Monsley realized that Dr. Lao was right and she tried to persuade Lepka, but Lepka had her arrested as a traitor instead and ordered her execution. Outraged by the underground residents who sheltered first Lao and now Lana, Lepka ordered the flooding of the underground residence with sea water. Lana was tricked by Lepka and gave herself up thinking incorrectly that Lepka would save the underground residents from the rising sea water.
On her way to execution, Monsley convinced the guards to let her see Conan first. Conan had already half-freed himself using his superhuman strength, and with a little help from Monsley, he escaped the Triangle Tower. Monsley, however, was shot and her fate unknown...
Conan rejoined Jimsy and Dyce in the underground only to learn that Lana had been captured by Lepka. With the rapidly rising water level, they realized that the only way to save the people was for the three of them to dive their way outside and open the shutter from the control room in the Triangle Tower...
Lana was taken to see Dr. Lao and she was horrified to learn that her grandfather had already lost his eyesight and hearing due to the torturing. Telepathy was the only way left to communicate with him. When Dr. Lao and Lana still refused to help Lepka , Lepka was outraged...
On their way to the control room Conan, Jimsy and Dyce managed to rescue the wounded Monsley from the firing squad. Together they headed to the control room when Conan noticed Lana near the top of the Triangle Tower...
Lepka put Lana at the end of a narrow retractable platform and extended the platform so that Lana stood in mid air with her hands tied at her back. Lepka was trying to make her yell out to Dr. Lao for help but she wouldn't. However she couldn't stand this way for long and she was about to fall when she heard Conan's call from below, asking her to hold on and to look down. She looked down and was elated to see that the shutter to the underground residence was opening...
Dyce and others had taken over the control room and opened the shutter to the underground. The underground residents all rose together in rage and stormed the Triangle Tower, seeking to defeat Lepka and save Dr. Lao. Conan meanwhile was racing to rescue Lana from Lepka, but when he reached the room where Lana was, Lepka had already taken Lana and tried to escape using the flying machine on the roof. Conan chased after them but Lepka stopped him by threatening to shoot Lana if he came any closer. Lepka and Lana got on the flying machine and started ascending when the flying machine was hit by a large needle-like structure Conan had just dislodged from the roof and threw upward with his superhuman strength. The flying machine was damaged and fire broke out. Conan then jumped on top of the flying machine and knocked Lepka unconscious. He carried Lana and jumped (more like flew) from the burning flying machine, which went out of sight for a moment and exploded.
Having disposed of Lepka, Dr. Lao, communicating through Lana, helped revive solar energy in the Triangle Tower in preparation for the evacuation of Industrian residents. Unbeknownst to them, Lepka escaped with his followers into the underground shelter where Giganto was kept. He tried to recharge Giganto secretly with the newly revived solar energy, but when the energy leak to the underground was discovered and cut off, Lepka led his men to occupy the control room in the Triangle Tower. Conan, Jimsy and Dyce meanwhile were away at the salvage ship trying to salvage the sunken Industrian ship so that it can be used for the flight from Industria... Lana and Monsley discovered Lepka and his men in the Triangle Tower and tried to inform Conan and others using the Falco, but it was too late. Lepka had already finished refueling Giganto and took off from the underground shelter. Witnessing this, Monsley tried to attack Giganto with the Falco but Giganto wasn't damaged due to its enormous size and strong fortification. Conan suggested they land on Giganto and try to do damage there. After they landed on Giganto, Conan, Jimsy and Dyce got off the Falco while Lana and Monsley glided back to Industria with the damaged Falco. Conan and company started wreaking havoc all over Giganto, causing fire to break out everywhere. Lepka was outraged and jettisoned the tail assembly of Giganto where Dyce and Jimsy were located. Lepka then tried to escape using a little escape craft. Conan stopped him in time and while Lepka's men were struggling to get onboard, Lepka got pulled off, leaving Conan alone on the craft. Soon after this Giganto went up in flame and plunged into the ocean below.
Back in Industria, people were getting ready to escape in the ship salvaged earlier by Dyce and others. There's no news from Conan and company but Lana and Monsley decided that they had to set sail or it would be too late. Soon after the ship left Industria, a great earthquake occurred and Industria sank into the sea, just as Dr.Lao had predicted earlier.
Half way to High Harbor, the Industrian ship found Jimsy and Dyce aboard the giant floating tail assembly of Giganto. Lana and others were rejoiced that they were safe but Lana was afraid for Conan. Dr.Lao instructed Lana to use her power of telepathy to try locating Conan. When she did, she found that Conan was drifting at sea not far from where they were, so they turned the ship and picked up Conan, much to the delight of all. Upon learning of Conan's return, Dr. Lao felt that his tasks were over, so he asked Conan to take care of Lana and died peacefully.
Some time had passed and the Industrians were well-settled in High Harbor. Dyce had finished repairing the Barrucuda and it was time for the launching ceremony, which also coincided with the wedding of Monsley to Dyce. Dyce, Monsley, Conan, Lana, Jimsy, Tara and many others had decided to sail to Remnant Island (Conan's home island) and settle there. But when they reached where the small Remnant Island was, they saw a large continent instead. Apparently the geological upheaval that destroyed Industria also pushed Remnant Island upward. Everybody was delighted to land on the new continent and all of them lived happily ever after