In 1532 a Spanish orphan named Esteban joins Mendoza, a navigator, and his associates Sancho and Pedro, in their search for one of The Seven Cities of Gold in the New World, hoping to find his father. They are joined on their quest by Zia, an Incan girl (who was kidnapped by Gomez, Gaspar, Perez and Mendoza), and Tao, the last descendant of the sunken empire of Mu (Hiva in the English dub).

The series is a mix of ancient South American history, archaeology, and science fiction. The travellers encounter the Maya, Inca, and Olmecs during their journey. They discover many lost technological wonders of the Mu Empire, including a solar powered ship (the Solaris) and The Golden Condor, a huge solar-powered ornithopter (mechanical bird), capable of traveling considerable distances under the sun's power alone. They are constantly pursued by antagonists Gomez and Gaspar, who are also in search of the Cities of Gold.

The Seven Cities of Gold were built by the Emperor of Hiva over fear of a global war which would destroy all civilization. Such a war did break out, destroying the Empires of Mu and Atlantis when they used the "Weapons of the Sun".^[5] The Seven Cities of Gold hold copies of books in their "Universal Libraries" as well as powerful artifacts, including the "Great Legacy", a portable fusion reactor. Other elements of this technology turn up in unexpected places, like the Solaris in Tao's home island, Esteban and Zia's medallions as keys to the Cities, or Tao's jar as an important piece of the Great Legacy.

Reminiscences of this ancient story are present in Inca legends written on golden quipu, which only Zia can read. This triggers an obsessive quest for the Cities of Gold on the part of the Spaniards Mendoza, Gomez, Gaspar and Francisco Pizarro.

Esteban seeks his long-lost father and is tied to Mendoza, who rescued Esteban from a sinking ship when he was a baby. Esteban seems to have a magical ability to make the Sun appear, which proves to be an invaluable asset throughout the series. Zia also seeks her father, from whom she was taken when she was six and brought to Spain as a gift to the princess. She has a medallion just like the one Esteban carries. Tao seeks signs of his ancestors; he possesses an encyclopedia about their lost technology and a mysterious jar which, according to the legend, only the high Priest of the City of Gold can open and proves to be the Great Legacy's cooling or control rod system. Mendoza, Sancho and Pedro are motivated by their search for gold, though Mendoza appears to be genuinely fond of the three children.

The Olmecs are the descendants of survivors of the global war who hid under their mountain. Only their elite were able to survive, suspended in cryogenic hibernation. The Olmecs do not appear to be human (or if they were once Human, it is implied that they have horribly mutated from the fallout of the nuclear war that destroyed their ancestors); they are short, thin and have pointed ears and enlarged frontal bones. They are highly intelligent but devious and selfish. Led by their king, Menator, the Olmecs seek an artifact called the "Great Legacy" in order to power their cryogenic systems, as well as samples of healthy cells from the children to combat their mutations and sterility. Their technology is generally inferior to that of the modern age, and they use weapons such as spears and swords. They do however maintain some elements of their advanced technological heritage such as the stasis and medical technology used to keep the elite of the Olmecs in suspended animation until an opportunity arises when they can be revived, powered by what appears to be a geothermal power system. This power system is destroyed in an escape by the children and Mendoza, starting a frantic search by the Olmecs for the fusion reactor core (the Great Treasure) hidden in the City of Gold. They also have a single flying machine that appears to use very similar technology to that of the Golden Condor. However, it is armed with some kind of particle beam or focused heat weapon of great power.

Eventually, the Olmecs succeed, at great cost, in taking control of the Great Legacy, but it begins to melt down without the moderation provided by Tao's jar. The resulting earthquakes and volcanism destroy the City of Gold. A world-threatening meltdown is avoided by the personal sacrifice of Esteban's father who, acting as the High Priest of the Cities, is presumed to be dead after replacing the jar. At the end of the series, Mendoza, Sancho, and Pedro, having salvaged some gold before the City's destruction, return to Spain - while Esteban and his friends set out across the Pacific in search of the remaining Cities.