In the year 2050, human society has achieved remarkable development through a newly harnessed energy source called e-Pulse, which is generated from human thoughts and emotions. This energy powers Sapotama, egg-shaped AI assistant devices that have become an indispensable part of everyday life for nearly everyone. However, lurking in the shadows of this technological utopia are Digimon, digital lifeforms that survive by consuming e-Pulse. When a Digimon drains all of a human's energy, the victim is left in a frozen, comatose state known as Cold Heart.

The story follows Tomoro Tenma, a cynical teenage boy living in a partially submerged, low-income district with his older brother Asuka. Tomoro possesses an unusually powerful and rare type of e-Pulse that causes Sapotamas to glitch. After a classmate falls victim to Cold Heart, Tomoro's own Sapotama malfunctions, giving birth to a gecko-like Digimon named Gekkomon. In the ensuing chaos, a powerful Digimon attacks, draining Asuka and leaving him in a Cold Heart state. Tomoro is then branded a criminal by the Ministry of Civil Protection, the government agency that conceals the existence of Digimon, and is forced to flee his home.

To survive and find a way to save his brother, Tomoro joins Glowing Dawn, a team of bounty hunters known as Cleaners who are hired to deal with rogue Digimon. The team is led by Kyo Sawashiro, a former member of the elite Five-Stars Cleaner unit who secretly dreams of coexistence between humans and Digimon. Other members include the hot-headed Reina Sakuya and her big-sisterly partner Pristimon, as well as the quiet and analytical young boy Makoto Kuonji and his observant bat-like partner Chiropmon. Initially, Tomoro rejects his partnership with the mischievous and self-serving Gekkomon, but he has no other options if he wants to recover Asuka's e-Pulse from the Digimon that stole it.

The series is set in a Crapsaccharine World, a dystopian society where the wealthy live in utopian floating structures called Shangri-La Eggs while the poor reside in the flooded, ruined areas below. The government actively hides the truth about Digimon and maintains control through the Cleaner system, placing bounties on humans who harbor Digimon. The opening episodes establish the Glowing Dawn arc, as Tomoro adjusts to his new life, learns to trust his teammates, and reluctantly bonds with Gekkomon. The subsequent Tactics arc introduces the Five-Stars, the top Cleaners in the world, and sees Glowing Dawn coming into conflict with a military-like Cleaner team called Tactics, uncovering a vast criminal conspiracy that reaches the highest levels of power. As the team confronts these threats, they begin to unravel the dark secrets behind the World Union, the corporation that manufactures Sapotamas, and the true nature of the e-Pulse energy that powers their world.