The Nova Corporation is the notorious company created and owned by Mr. Mech. It manufactures mech parts for the gladiators fighting in Mr. Mech's Arena to create their own mechs. They are considered a primary antagonist in the first season, but fade away as Cyblains are revealed in Season 2.
Unlike many of the other concepts in M³, The Nova Corporation was not introduced in the manga. In fact, there is no trace of it until the anime. This is due to the fact that M³'s creator, Hakima Futamosho, had no original intent for a corporation to be placed within the world at the time of Battle of Royales. However even with his discontent, his publishing company, Nova Incorporated, tried to push it. They failed to add it within the manga due to executive decisions and Futamosho being extremely stern over the subject. When Hakima was working on the anime adaptation of Mr. Mech, he was given much more creative freedom and was allowed to explore several things he hadn't before. To get back at his publishing company for demanding changes to his story, he named the evil corporation in the show after them.
It's unknown when Nova started, but it is well known that it would set the domino effect for the Cyblain overlord Mr. Mech to take over Earth. After popularizing the mech design for sport, transportation, and working use, the Nova Corporation was able to easily abuse its power and take over the planet Earth. Its true purpose was to create mechs to use humans as slaves for the Cyblains and it did just that. After the death of Mr. Mech, the Nova Corporation was disbanded, allowing humanity to be freed.