Muteking emerges from two distinct narratives. In the original continuity, twelve-year-old Rin Yuki lives in fictional Yon Francisco. He champions his scientist father's theories of an imminent alien invasion, dismissed by others. Rin meets Takoro, an extraterrestrial deputy sheriff tracking the Kurodako Brothers—four shapeshifting criminals from the Octopus Planet plotting to conquer Earth. Takoro grants Rin transformation abilities via a mouth-emitted ray. As Muteking, Rin gains enhanced physical and mental prowess, adopting a superhero persona who primarily fights crime using roller skating skills. He retains his ordinary personality, favoring play over academics, and wears headphones with a Walkman.

Rin thwarts the Kurodako Brothers' schemes, often born from comical misunderstandings of human life (like believing humans evaporate when wet). His allies include Takoro—who occasionally causes mishaps like accidentally creating "Mute Queen"—and the sentient, clock-shaped spaceship Hotke Saucer, providing tactical battle support. Rin's family remains largely unaware of his dual identity, with his police chief mother dismissing Muteking despite encountering his exploits.

In the reboot continuity, Muteki, Rin Yuki's great-grandson, becomes the primary Muteking wielder after moving to Neo San Francisco to live with his grandmother. Muteki encounters DJ, an extraterrestrial entity enabling his transformation through an alien boombox. This version channels powers via Octian Cells within Muteki's body, emphasizing dance and musical performances to combat threats. Muteki displays inherent rhythm skills and persistence, especially in pursuing romance, though he exhibits obliviousness to danger. His transformations trigger large-scale environmental shifts toward positivity, involving elaborate musical numbers.

Muteki confronts antagonists led by the CEO of tech corporation Octinq, seeking to engulf the city in darkness using advanced technology. Muteki navigates personal challenges like public fame and strained relationships, exacerbated by the CEO's manipulations. A significant evolution occurs when Muteki and DJ fuse into "Mirror Muteking," utilizing the "Super Hyper Dance" to purify corrupted entities like Muteking Black. This fused form represents their ultimate cooperative power, resolving the primary conflict.

Both iterations share core elements: a young protagonist gaining heroic abilities through alien intervention, comedic yet high-stakes battles against technologically adept foes, and themes of family legacy. The original emphasizes roller-skating action against episodic villain schemes, while the reboot focuses on dance as a transformative force against systemic technological threats.