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)

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.

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.

The Band of the Hawk has dwindled in the year since Guts left them on his journey to forge his own destiny. Unaware of their fate, Guts returns to the Hawks—now being led by his former ally Casca—after a rumor about them passes his way. Once the saviors of the kingdom of Midland, the Band of the Hawk are now hunted as they desperately fight for their lives while plotting to free their leader, Griffith, after he was imprisoned for committing treason. But the man they save is far from the Griffith they remember. Griffith is a shell of his former charismatic self after a year of continuous, horrific torture. No longer able to walk, speak, or even hold a sword, he has nothing but the small, strange trinket, the Crimson Behelit, that will not leave him. The entire Band of the Hawk want to rise to greatness once more, but how much are they willing to sacrifice to return to their past glory? It doesn't seem possible, but when Griffith's heart darkens and a solar eclipse blackens the sky, the Behelit offers a choice that will leave the Band of the Hawk with a blood-soaked fate that will haunt them for the rest of their days.