Nene is the main villain of Blue Dragon. He is the leader of the Gran Kingdom, and flies around the world causing destruction and despair for seemingly no reason. He initially appears as an old man, has a frog-like pet named Deathroy who is chained to his shoulder and always repeats the end of his sentences, and his second-in-command is General Szabo. Nene has a "shadow" that is a red version of Shu's Blue Dragon, which turns into a Chimera later in the story.
At the start of the game, he is controlling the "Land Shark" that is terrorizing the village where Shu, Kluke and Jiro live, and in an attempt to stop the Land Shark they wind up meeting Nene on board his ship and barely survive a confrontation with him, getting stranded in the middle of nowhere. Along the way home, they continue to encounter Nene's path of destruction, and eventually find that the village has been destroyed as well, and the people are migrating to where it is safer.
At the end of the second disc, Nene steals away the main characters' shadow guardians to complete his own and achieves full power, losing his aged appearance and becoming much younger (they later regain use of the shadows but Nene keeps all his power as well). Towards the very end, it is revealed that he had intended the children to acquire and train their shadow guardians from the beginning, as they were originally all part of his shadow but the overuse of the magic was draining his soul and making him old, and he used the children to re-power his shadow with the energy from their stronger souls.
Also during the final confrontation, Nene reveals that Zola, one of the main party members, had actually been working for him all along and was the mysterious voice the children heard when they got the light spheres that gave them their shadow guardians, and after Nene is defeated he asks Zola to take back the shadows and give them to her again. However, Zola has a change of heart and kills Nene instead.
After that, it turns out that Nene's pet Deathroy was actually "Destroy", the ancient monster mentioned earlier in the game who destroyed a past civilization, and he turns into a giant monster for the game's very last boss battle.