Many years ago, after the end of a bloody world war, mankind took shelter in six city-states that were peaceful and perfect... at least on the surface. However, Shion—an elite resident of the city-state No. 6—gained a new perspective on the world he lives in, thanks to a chance encounter with a mysterious boy, Nezumi. Nezumi turned out to be just one of many who lived in the desolate wasteland beyond the walls of the supposed utopia. But despite knowing that the other boy was a fugitive, Shion decided to take him in for the night and protect him, which resulted in drastic consequences: because of his actions, Shion and his mother lost their status as elites and were relocated elsewhere, and the darker side of the city began to make itself known. Now, a long time after their life-altering first meeting, Shion and Nezumi are finally brought together once again—the former elite and the boy on the run are about to embark on an adventure that will, in time, reveal the shattering secrets of No. 6.

The bustling metropolis of Kansai, where cybernetic screens litter the neon landscape, may seem like a technological utopia at first glance. But in the dark alleys around the brightly-lit buildings, an unforgiving criminal underbelly still exists in the form of fugitives known as Akudama. No stranger to these individuals, Kansai police begin the countdown to the public execution of an infamous Akudama Cutthroat, guilty of killing 999 people. However, a mysterious message is sent to several elite Akudama, enlisting them to free Cutthroat for a substantial amount of money. An invisible hand seeks to gather these dangerous personas in one place, ensuring that the execution is well underway to becoming a full-blown bloodbath.

Maquia is a member of a special race called the Iorph—mystical beings who can live for hundreds of years and remain separate from the lives and daily troubles of mankind. However, Maquia has always felt lonely despite being surrounded by her people, as she was orphaned from a young age. She daydreams about the outside world, but dares not travel from her home due to the warnings of the clan's chief. One day however, the outside world finds her, as the power-hungry kingdom of Mezarte invades her homeland. They already have what is left of the giant dragons, the Renato, under their control, and now their king wishes to add the immortality of the Iorph to his bloodline. The humans and their Renato ravage the Iorph homeland and kill most of its inhabitants. Caught in the midst of the attack, Maquia is carried off by one of the Renato that has gone berserk. It soon dies, and she is left deserted in a forest far from home, now truly alone save for the cries of a single baby off in the distance. Maquia finds the baby in a destroyed village and decides to raise him as her own, naming him Ariel. Although she knows nothing of the human world, how to raise a child that ages much faster than her, or how to live with the smoldering loneliness inside, she is determined to make it all work somehow.

Alcia is a world governed by Count: numbers engraved on a person's body, representing any number related to their life. These Counts determine a person's social status and power in Alcia. If a Count reaches zero, the person is sent to the Abyss, a place rumored to be worse than death. Hina, a traveler whose Count is based on the distance she traveled, witnessed her mother get dragged down into the Abyss. Determined to fulfill her mother's last wishes, she sets off on a journey in search of the legendary Aces—heroes of the war that happened three hundred years ago, bearing a white star next to their Count. While wandering around, Hina encounters Licht Bach, a mysterious masked man with negative Count, and Nana, the owner of a tavern. In the midst of having a good time, Hina is tricked into a battle with a military soldier. However, despite his negative count, Licht rescues Hina and reveals that he has another count, one with a white star, one of a legendary Ace. Plunderer follows the journey of Hina and other inhabitants of Alcia as they discover the truth about their world, the Abyss, and the legendary Aces.