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 Jujinkai (a half-man, half-beast race). Once every 3,000 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.

Two years have passed since the Great War. Akito and Yurika have vanished. The Jovians and the Earthlings have joined forces and Ruri is now captain of Nadesico B. As the popularity of Boson Jumping grows, a vast transportation network has been developed. Dubbed the Hisago Plan, this network of Chulip portals holds the answers to the mysteries behind Bose particles and their power. If those secrets should fall into the wrong hands, it could mean big trouble. And big trouble there is. A Martian splinter group has launched an offensive, leaving the United Forces befuddled and desperate. So much so, in fact, that the former crew of the Nadesico is called back to active duty for a special unsanctioned mission-to save us all. Does this menagerie of misfits have what it takes? Who will win the race for the Boson technology? And what the heck happened to Akito and Yurika?

Masane Amaha and her daughter Rihoko are on the run from a government child welfare agency that wants to take Rihoko away from her mother. They are caught and Rihoko is taken away. Meanwhile, Masane is attacked by an advanced weapon that can disguise itself as a human being. When faced with the danger, a strange light emits from her wrist and she transforms into a powerful being. She becomes involved in a power struggle between powerful organizations, with her at the center of their attention because she holds the greatest power of them all, the legendary Witchblade.

UFOs appear on Earth, and people who actually see them suddenly find that their blood has turned blue. Soon panic and hysteria result in the new "blue-bloods" being persecuted by the rest of mankind, and eventually certain all-too-familiar measures begin to be taken against them.

A top-secret weapon escapes from military custody ready to destroy its pre-programmed target. The nosy freelance reporter who shows up to cover the story lands herself at the center of something even more dangerous than the international scandal she signed up for.

An adolescent with the ability to control a looming war-golem becomes entangled in the Experts of Justice's fight against the infamous group Big Fire.