"Desert Punk" is set in a post-apocalyptic future where Japan has become a vast desert wasteland. Society has regressed to a feudal state, with survival depending on resourcefulness and cunning. The protagonist, Kanta Mizuno, is a skilled mercenary known as "Desert Punk," renowned for his sharpshooting and survival skills. Despite his reputation, Kanta is often driven by base desires, such as money and women, which frequently lead him into trouble.

The narrative begins with Kanta taking on various odd jobs, ranging from escort missions to bounty hunting, often clashing with rival mercenaries and bandits. His life takes a turn when he encounters a young girl named Kosuna, who idolizes him and insists on becoming his apprentice. Initially reluctant, Kanta eventually takes her under his wing, though their relationship is fraught with tension and mutual exploitation.

As the story progresses, Kanta becomes embroiled in larger conflicts involving powerful factions vying for control of the desert's scarce resources. One such faction is the Great Kanto Desert Government, which seeks to maintain order and stability, often at the expense of individual freedoms. Another is the enigmatic and ruthless Rain Spider Clan, a group of elite mercenaries with their own agenda. Kanta's interactions with these factions reveal a complex web of alliances, betrayals, and shifting loyalties.

Throughout the series, Kanta's character is explored in depth, showcasing his pragmatism, resourcefulness, and occasional moments of vulnerability. Kosuna, on the other hand, evolves from a naive admirer to a more independent and capable individual, though her loyalty to Kanta remains a central theme. The dynamic between the two characters is a key element of the story, blending humor, action, and moments of genuine emotional depth.

The plot is driven by a series of episodic adventures that gradually build into a larger narrative arc. Key events include Kanta's confrontations with rival mercenaries, his involvement in political intrigue, and his quest for personal gain, which often puts him at odds with both allies and enemies. The series balances action-packed sequences with strategic planning and tactical combat, highlighting Kanta's ingenuity and adaptability in a harsh and unforgiving environment.

"Desert Punk" also delves into themes of survival, morality, and the human condition in a world where traditional values have eroded. The desert setting serves as a metaphor for the characters' struggles, emphasizing the importance of resilience and adaptability. The series concludes with a resolution that ties together the various plot threads, providing closure to Kanta's journey while leaving room for interpretation regarding his future.