Daiya Tsuwabuki is a boy in junior high who is known as the town liar. He claims that five years ago, he was saved by a large mechanical dragon when he and his father were attacked at sea by mechanical beasts.
Daiya meets the crew of Daiku-Maryu, which includes Lulu, Gaiking's supporter; Captain Garis; Vice Captain Rosa; Shizuka and Daimon in charge of the engine room; and Puria, the pilot of Stinger and the ace fighter of Daiku-Maryu.
Daiya learns that for their fight against the Darius Army, they have to go to the other world at the core of the earth, and Captain Garis gives Daiya some time to go say goodbye to his mother.
In order to return to Darius, Daiku-Maryu must go through Death Cross Point and mend the subspace in order to prevent the enemy from going to the surface.
Daiku-Maryu arrives in Darius and goes to a regional city called Paltegona to stock up on food and supplies. Captain Garis orders Rosa to take Daiya and Puria into town with her in order to give them an opportunity to start getting along.
Captain Garis temporarily assigns Daiya to five sections on the ship to decide which section he will join permanently. On the first day of the three-day trial, Daiya has a lot of trouble with the tasks of each section, especially when he has to run around Daiku-Maryu running errands for his bosses.
Daiku-Maryu docks at a tropical island where the crewmembers enjoy some beach time. Then from the other side of the island, they hear the sound of wild Demon Beasts, which are indigenous Demon Beasts that have not yet been made evil by the Darius Army.
On their way to their fort in Ohmazan, Daiku-Maryu takes a break in the Kanalups Mountains. Puria, who gets into a foul mood watching Daiya and Lulu having a great time, decides to play a prank on Daiya and puts Pelps, mosquito-like insects of Darius, into his tent that night.
One day on their way to the Ohmazan fort, Daiku-Maryu is attacked by a giant turtle beast, Domega. During the battle, Daiya and Lee try to combine Gaiking and Serpent to become Buster Gaiking, but Lee fails in the attempt.
As Daiku-Maryu approaches the dark continent of Arkholand where the Darius Army headquarters is located, Lulu starts having nightmares about her childhood and the black flame.
One day, Grotecter warships of Northern General Noza fly past Daiku-Maryu. They are on their way to create another Death Cross Point, the hole that connects to the world above the surface.
While Grotecter warships are forming Death Cross Point, Noza challenges Daiya to another duel. Daiya goes against Garis's order and accepts, even though he is daunted by Noza's strength.
After the battle with Noza, the captain and Daiya fall ill, and Daiku-Maryu, as well as Stinger and Serpent, are badly damaged. Captain makes Lulu command the ship in his absence, and reveals his identity to Daiya.
During a battle in the air, a civilian airplane asks Daiku-Maryu for help, and Lulu agrees to let him come onboard. The pilot, a Darius man named Jan, demands to be taken to the surface world and tries unsuccessfully to hijack Daiku-Maryu.
One day, Lee goes on a recon mission and saves Vestarnu, who is being attacked by droid soldiers at Proist's secret quarry. She gets gunpowder in her eyes and becomes temporarily blinded.
Dick attacks Gaiking to get to the enemy, and while the enemy falters, Gaiking counterattacks. Although they managed to get through the battle, everybody is furious at Dick for his dangerous tactic.
Powerless against the enhanced Steel Beast, Stinger, Serpent, and Killjaguar retreat to Daiku-Maryu for the time being, but they learn that Proist ordered a public execution for Gaiking.
One day on a deserted island, Garis proposes a race to go find Windarium, a mineral ore that can counterattack Darius's ice beam. The winner will become the Daiku-Maryu captain for a day, and ten crewmembers decide to participate in the race.
Lulu starts reading people's fortunes when one day, she predicts that Bry, the rebel fighter and Daiku-Maryu supporter, will reunite with someone special. Meanwhile, Daiya gets jealous watching her read fortunes for other people.
One day, Yanma, Haccho, and Booby, in an attempt to prove their usefulness, force themselves onto Gaiking with Daiya. But Gaiking gets captured by the enemy, and Daiya and the trio are taken back to the enemy warship.
The Daiku-Maryu crewmembers start seeing pink hippos everywhere on the ship. Dr. Franklin informs them that they are hallucinations from Limitation Syndrome, which occurs when people feel stressed out.
The Daiku-Maryu idol contest enters the final round in which the candidates become an idol for the deciding popularity vote. They each make a performance that will attract the crew's attention.
Concerned about Captain Garis's odd behavior, Dick and Daiya take off on a surveillance mission and land in a ruined city. There, Dick runs into Proist, and Daiya into Noza.
Daiku-Maryu gets attacked by Vestarnu and her Steel Beasts, and Lulu gets kidnapped. To get her back, Proist tells Garis to come alone to the place where he hid Tenku-Maryu.
Dick intervenes just in time and takes the blade in the shoulder instead of Garis. Lulu gets taken away again by Proist, and Garis and the others return to Daiku-Maryu. There, Sakon, Daimon, and Franklin reveal Garis and Lulu's secret.
Daiku-Maryu docks by a beautiful lake, and the crewmembers enjoy a moment of relaxation. There, Daiya compares his friend Naoto and his video games to their battle against Raiking and Vulking.
Lee infiltrates Daichi-Maryu and finds a way to undo the brainwash on Vestarnu. He tells Daiya to do the same thing to Noza. Shizuka and Sakon overtake Tenku-Maryu, and now the three Maryus and the three Giants of Flame are under their control.
Daiya and Puria are blown away to the surface on Gaiking's torso and Superior Stinger. They find themselves on a deserted island but don't have enough flame in their machines to fly anywhere.
When Kaikink is fixed, more Steel Beasts attack the cargo ship. Then suddenly, Killjaguar and Daiku-Maryu show up and join the battle. They destroy the Steel Beasts, and Daiya and Puria go back onto Daiku-Maryu.
Daiku-Maryu returns to Darius with a special missile that creates Death Cross Point. They join up with Lee and Vestarnu on Daichi-Maryu and head toward Darius Capital.
Emperor Darius contacts Lulu and asks her to stop Proist. He asks for a meeting and says he will bring Daiya's father with him. Lulu thinks that it may be a trap, but decides to meet him anyway.
Proist puts Daiya's dad in a pod inside the Super Maryu Beast, Final Dvorzak. The pod is connected to the beast's heart with cords, and when Daiya tries to pull it out, some cords break, making his dad feel excruciating pain.
Lulu is devastated over Dick's death and refuses to command the ship until Rosa makes her come to her senses. Daiya returns to Daiku-Maryu for refueling and have a tearful reunion with his father.
Proist comes back to life after her four generals sacrifice their lives for her. She shows up in Daiku-Maryu, and turns into a demon out of jealousy and rage when she sees Daiya with his dad and Lulu with her dad, Garis.
