The series centers around Medabots, artificially intelligent robots, whose purpose is to serve humans. The series begins with a ten-year-old boy named Ikki Tenryō, who wants to become a champion of the World Robattle Tournament. However, Ikki is unable to afford a Medabot, and his parents refuse to buy him one. However, he manages to get enough money to buy an outdated model, and, with a bit of luck, he finds a medal in a river. Ikki quickly inserts it into the Medabot he purchased named Metabee. The only problem is that the medal he found gives Metabee a severe attitude problem (a problem rarely seen in a Medabot), which leads Ikki to think he is defective. However, this theory is proven wrong later in the series, as it is revealed that Metabee actually has a "rare" medal.

The rare medals were kept secret by the Medabot Corporation, as very little was known about them. However, a Medabot with a rare medal would be able to call upon an attack called the "Medaforce". In the manga, the Medaforce is a form of medal mind control, as explained by Dr. Aki in the third graphic novel of Medabots. In the cartoon however, it is shown as a way of increasing the power of the Medabot's special skill into a focused beam attack.

Another important aspect is the story of Henry, the store clerk who sold Ikki Metabee. We find out that he is, quite obviously, Phantom Renegade. A running gag of series was Henry almost telling everyone he is The Phantom, with no one ever discovering this fact. We are then introduced to Space Medafighter X, who is another one of Henry's secret identities, the number one medafighter in Japan. Later, during the World Finals, he rarely shows up to the fights, instead sending substitutes and working behind the scenes. This being because he supposedly started The Ten Days of Darkness, which occurred eight years before the events in the series during the World Robattle Cup when Henry fought as Hikaru Agata with the original Metabee ( however, the medal was different). The Medabots went on a rampage during the Ten Days of Darkness, which stopped when Hikaru Agata was forced to kill his Medabot by destroying his medal.

At the end of the second season, it is revealed that Victor (a medafighter for Team Kenya and Warbandit's owner) was helping Dr. Meta-evil to get medals during the tournament. During the finals, Metabee and Warbandit continue to fight, even with their partners lost and their bodies damaged. It is during this event that Dr. Meta-evil starts his plan using Metabee and Warbandit's medals; trapping them both in a dream. However, Ikki manages to get Metabee to wake up from the dream, while the other medabots, free now, help Metabee to fight against Dr. Meta-evil. Ikki must also stop the plans of the nefarious "RubberRobo Gang".

Later in the series, Medabots are found to be actually thousands of years old; remnants of an ancient civilization who called themselves Medalorians. The Medalorians were obsessed with war, and to become more effective warriors they fastened metal armor to themselves. However, their wars decimated the civilization, and the survivors coded their memories onto hexagonal pieces of metal. These, "Medals", cloned and mass-produced by the Medabot Corporation (a corporation founded by Dr. Aki), are the Medabot equivalent of a brain and soul. The original medals, referred to as "rare" medals, are kept in storage because of the extreme power they have.