Legend has it that the human race is not the only dominant civilization living on Earth. Two other races exist in this world: the Makai (a demon race) and the Juujinkai (a half-man, half-beast race). Once every 3000 years, a supreme being known as the Choujin (Overfiend) will emerge and bring balance to all three realms on Earth. In present-day Japan, after 300 years of endless searching, a Jujinkai named Amano Jyaku has discovered the presence of the Choujin inside high school slacker Tatsuo Nagumo. But now, Amano - along with his sister Megumi and their sidekick Kuroko - must protect Nagumo and his new girlfriend Akemi Ito from the Makai, who believe that Nagumo is not the Choujin, but an evil entity bent on destroying all living beings on Earth.

An army of invading aliens attack the peaceful land of Lyon with lust and carnage on their minds. Only the combined forces of Swordsman Zeke, Swordswoman Neris and the psychic Flare stand between the sadistic Glode and his total subjugation of the people of Lyon. In Flare 2, the forest of Lyon becomes host to a malevolent force that consumes all who trespass its borders. When Lady Neris and her brother Eon disappear while investigating, it is up to Flare to discover what new evil lurks in the heart of Lyon!