Young Ruuji Familon finds a Liger-type Zoid during a salvage mission. Initially, the village is attacked by Bio-Raptor Bio-Zoids, and later a Bio-Megaraptor. After the village generator is destroyed in combat, Ruuji takes the Murasame Liger Zoid and leaves the village alongside Ra-Kan and Rei Mii to find a generator mechanic or the village will be destroyed. Through his journey Ruuji learns he must fight against Digald.

Zoids: Genesis тривав 1 сезон. Нових епізодів не заплановано.