Ten years after the destruction of Jamahl, Earth has remained in a state of peacefulness. The Earth Academia has become the Cosmo Academia, where Kai Takuya, the original Blue Beet, and Guru, the insect elder work on a newer version of Insect Armor in the event of another threat to the Earth. A Cosmo Academia exploration submarine comes across a fissure in the ocean floor, out of which rises a giant floating fortress. Melzard, an ancient tribe has awakened where it had laid dormant for millions of years, and seeks to destroy mankind. The giant Mother Melzard, ruler of the Melzard Tribe dispatches her sons, Raija and Dezzle. Raija and his comrade Miorla command land-dwelling animal monsters. Dezzle and his companion Dord command sea-dwelling animal monsters.

Guru infuses the new Insect Armor with Insect Power, creating the three Command Voicers. Kengo and Ran, who have been selected to wear the new armor, become B-Fighter Kuwagaa and B-Fighter Tentou. Ran and Kengo run after the remaining Command Voicer flies out the window. Meanwhile, a high school student named Kouhei and his sister are attacked by Elebammoth. The Command Voicer chooses him and Kengo and Ran are shocked that this highschool student is chosen to be B-Fighter Kabuto. He changes into Kabuto and the three of them, hence become a team. The B-Fighters convene at Cosmo Academia headquarters, under the guidance of Professor Osanai and Bitto, the intelligence computer. They operate the powerful Neo Beet Machines, to fight against Melzard's hordes of Gidorba and aerial Fly Gidorba fighters.

When Mother Melzard's most powerful child Hebyuuza proves to be too much for the B-Fighters, the first generation B-Fighters come to help them. But Hebyuuza infects all six of them with her special cells before she is destroyed, and as the cells invade their Insect Armor the B-Fighters are controlled into battling one another. Taking advantage of this, Raija sends Driceraija, to attack the helpless B-Fighters. To prevent themselves from dying, the B-Fighters de-transform. Osanai and Bitto discover that cold will expel the cells out of the armor. Once they do so, the B-Fighters kill Driceraija. Raija, enraged at this defeat, challenges Kabuto to a duel and is beaten by him. After that, Takuya reveals the reason he and his team returned was that eight golden medals have fallen to different areas of the Earth. They soon discover four of them went to individuals that become B-Fighters. The other four medals were ingested Mother Melzard and she gives birth to the B-Crushers.