In the year 1999, humanity begins to advance beyond the solar system. The planet Gishin, led by the Emperor Zule, which aims to conquer the galaxy, runs into conflict with Earth. He targets Earth for elimination and to do this, he sends a baby called Mars to live among humanity. Accompanying the baby is a giant robot named Gaia, which utilizes a new power source strong enough to destroy an entire planet. As planned, Mars is expected to grow up, where he will activate the bomb within Gaia to fulfill the mission of destroying the Earth. However, when Mars arrives on Earth his is adopted into a Japanese family and given the name Takeru. Seventeen years later, Takeru would grow up with a love for humanity and refuses to detonate the bomb as ordered by Zule. However, if Takeru was to die, the bomb within Gaia would explode destroying the earth. Takeru possesses psychic powers ( ESP ) and decides to join the Earth defense forces and becomes a member of the Crasher Squad (an elite space defense force) where he and his friends take a last stand against the Gishin's attack. The relationship of Takeru with his brother Maag, which fate would have it, pitted the two against each other in the war. Unknown to the Gishin five other robots were created in secrecy along side Gaia by Takeru's father and sent with Gaia to protect Takeru. Whenever Earth is in danger, Takeru is able to summon the five other robots to combine with Gaia form the giant robot Godmars. The five other robots are Sphinx, Uranus, Titan, Shin and Ra.

In order to prevent the catastrophe called the Grand Fall, Rid Hershel and his companions Farah, Keel and Meredy have obtained the three Greater Spirits ("Craymels" in the game version) of Inferia. En route to Mount Farlos, Rid is kidnapped by the bounty hunter Marone Blucarno, and the party is compelled to head to Belcarnu, an archipelago far from the major cities of Inferia. A series of adventures forces them to remain on the islands, where a more immediate threat to Inferia sleeps.

The story centers around an evil counterpart of Arale created by Dr. Mashirito named Abale.

In this series the story continues after Katta Kirifuda defeats the YA.RA.SI band and also gains back his popularity by defeating Leo and his sidekick Nai Minamimo. In this series Katta will use a new race of Outrage creatures against the opposing new race of Oracle deck users. Also in the creature world a new time era will start off. (Source: Duel Masters Wikia)