Take place 2 years after the last episode of the TV series. Detective Sonia Summers are tracking Bem and the others. She reunited with Belo, who is fighting a dark organization alone. He brought her to Bem, but Bem doesn't remember anything and living in the city as an ordinary employee... or that is what he thought he was.

It is the dark century and the people are suffering under the rule of the devil, Vandel, who is able to manipulate monsters. The Vandel Busters are a group of people who hunt these devils, and among them, the Zenon Squad is known to be the strongest busters on the continent. A young boy, Beet, dreams of joining the Zenon Squad. However, one day, as a result of Beet's fault, the Zenon squad was defeated by the devil, Beltose. The five dying busters sacrificed their life power into their five weapons, Saiga. After giving their weapons to Beet, they passed away. Years have passed since then and the young Vandel Buster, Beet, begins his adventure to carry out the Zenon Squad's will to put an end to the dark century.

Young detective Sonia Summers has been transferred to the outskirts of the port city Libra after stirring up trouble with her superiors. Libra is separated into two sectors—the Upper, the center of wealth and politics, and the Outside. The Outside is home to crime, corruption, and curious incidents involving monstrosities or youkai. Each case that Sonia works on seems to implicate the involvement of these mysterious creatures. Sonia crosses paths with three peculiar humanoid youkai—Bem, Bela and Belo—who seek to protect humans and fight against the evil youkai that terrorize them. Living as Youkai-Ningen, they are excluded by other youkai for their human-like lifestyles, and rejected and hurt by humans when they reveal their true forms. Despite the hardships they face, these three Youkai-Ningen secretly live among humans, continuing to pursue their dreams of one day becoming human as well.

Beast Wars Second features a new cast of characters set many years in the future, who travel to a post apocalyptic Earth now known as the planet Gaia. The Cybertrons, led by Lio Convoy, are sent to the planet to investigate an unusual change in the planet’s behavior and thus thwart the Destrons, led by Galvatron, who seek to consume the planet’s rich source of energy called Angolmois. (Source: Karyuudo Fansubs)