Formerly a human, the Doctor Man becomes a robot and builds an empire of Robots but the Biomen appear to fight them. Mason, one of Doctor Man's generals, with Psygorn's help, succeeds to kill Yellow Four (Mika), but she is replaced by Jun who becomes the new Yellow Four. Doctor Man creates Prince as his son and heir, but he is destroyed by the Biomen. Later, the Neo Empire Gear loses two Beastnoids : Messerjū and Aquaiger, when Doctor Man decides to sacrifice the Five Beastnoids in a plan to kill the Biomen but it fails. Mettzler and Psygorn survive and are upgraded by Doctor Man. Monster finds Zyuoh's pieces and begs Doctor Man to rebuild and upgrade him too. Doctor Man accepts.

Later, Bio Hunter Silva arrives on Earth. He wants to destroy the Biomen, because they possess Bio Particles, but he is not ally with the Empire Gear. Doctor Man tries to ally with him but Silva refuses. Then, Doctor Man will search to take Balzion, Silva's robot to defeat the Biomen once and for all. He succeeds it but Monster and Zyuoh died. He sends Fara with Faracat and Mettzler to kill the Biomen but the plan fails and Mettzler and Fara are destroyed.