After conquering the galaxy, mankind has reached its apex and is now on a steady decline. The resources of the universe are diminishing, and around 500 billion humans begin to return home to Earth. Thus begins a war between the various factions of humans for control of the planet. Eventually, an authoritarian government known as the Gaia Sanction prevents the re-population of Earth. Captain Herlock was one of the Elite Wing who was tasked by the Gaia Sanction to defend the Earth. His fleet of ships was unstoppable under his command. However, the Gaia Sanction allows a diplomatic elite to immigrate to Earth, which angers Herlock. He goes rogue and fires upon the diplomats and the rest of his fleet. He decides to unleash dark matter on the planet to make it uninhabitable, but also becomes engulfed in it which immortalizes him. One hundred years have passed, and the legendary Captain Herlock is still at large, with only the Arcadia under his control. The Gaia Sanction continues with their plans for control over the Earth, while hiding its true state. But Captain Herlock is preparing for one final showdown with them, which will determine the fate of the world!

Tatsumiyajima is the central island in the middle of a small cluster of islands, in a sleepy backwater of the Japanese isles. Not much happens there, and the island's young people go to school knowing that their lives are likely to remain peaceful and undisturbed. Or so they have been taught... but the truth is different. The fate of mankind is on the line, and Tatsumiyajima is the last line of defense against a hostile and incomprehensible enemy. At the center of it all, fighting for Humanity's continued existence, is the giant robot Fafner, the dragon that guards this final treasure of mankind.

Sung Jin-Woo, dubbed the weakest hunter of all mankind, grows stronger by the day with the supernatural powers he has gained. However, keeping his skills hidden becomes more difficult as dungeon-related incidents pile up around him. When Jin-Woo and a few other low-ranked hunters are the only survivors of a dungeon that turns out to be a bigger challenge than initially expected, he draws attention once again, and hunter guilds take an increased interest in him. Meanwhile, a strange hunter who has been lost for ten years returns with a dire warning about an upcoming catastrophic event. As the calamity looms closer, Jin-Woo must continue leveling up to make sure nothing stops him from reaching his ultimate goal—saving the life of his mother.