The second series is to follow the events of the second video game, focusing on the lost continent of Mu. The ancient civilization vanished ages ago, and a few of its remnants still exist as myths and legends called UMAs (unidentified lifeforms). The UMAs begin merging with humans in order to search for the treasures of Mu, the powerful ooparts, which will give them the power to revive Mu. After Subaru and War-Rock encounter several unusual enemies, they meet a professor named Doctor Orihime who sends them on a quest to find the ooparts and stop the UMAs. Using the ooparts, Rockman is able to take new forms, including Thunder Berserk, Fire Dinosaur, and Green Shinobi.

Natural disasters have devastated planet Zi, killing off almost all life. A thousand years later humans have gradually re-established civilization, salvaging ancient Zoids through diving and mining efforts. In a village whose most previous item is a giant sword which they worship as a holy symbol. A teenage boy discovers an ancient Liger-type Zoid while on a deep water salvage operation. Suddenly the village is attacked by skeletal Bio-Zoids intent on stealing a powerful generator located in the village. Our teenage hero awakens the Liger and discovers that the town`s sacred sword is the Liger`s weapon, together they fight off the mysterious Bio-Zoids. At least for now...

Habahiro Hige awakens at his desk at work, but much to his surprise, he has become a baby! To make things stranger, Iori Wakabayashi walks in wearing a school uniform but doesn't recognize him as the baby. Upon being picked up and held by her, Hige discovers that he doesn't just have the body of a baby but the mind of one as well.

The story follows a young genius university professor who is able to learn any language. He is asked to decipher a code used in wireless communication: the Luger Code, developed by werewolves, enemies to mankind. Startled to find that he cannot decipher the code and desperate to study it, the professor embarks on a journey to capture a living werewolf to aid him.