"Chocolate Underground" is a 12-episode anime series set in a dystopian future where the government enforces strict dietary regulations, banning all forms of sweets and confectionery. The story centers on two teenage boys, Huntly and Smudger, who live in a society where the Good For You Party has outlawed chocolate and other sugary treats, deeming them harmful to public health. The regime enforces its policies through propaganda, surveillance, and harsh penalties for those who defy the ban.

Huntly and Smudger, disillusioned by the oppressive regime, secretly establish an underground resistance movement called the "Chocolate Underground." They begin producing and distributing illegal chocolate to those who crave it, operating in secrecy to avoid detection by the authorities. Their efforts gain momentum as they recruit like-minded individuals, including their classmate Hayley, who becomes a key ally in their mission. The group faces constant danger from the government's enforcers, particularly the zealous Inspector Archibald, who is determined to eradicate all traces of chocolate and crush the rebellion.

As the story progresses, the boys' actions inspire a growing number of citizens to challenge the government's authority, leading to a broader movement against the oppressive regime. The series explores themes of resistance, freedom, and the power of collective action, as the characters navigate the risks and moral dilemmas of their rebellion. The narrative balances moments of tension and danger with lighthearted humor, particularly in the interactions between Huntly and Smudger, whose contrasting personalities—Huntly's cautious nature and Smudger's impulsive tendencies—drive much of the story's dynamics.

The climax of the series sees the Chocolate Underground gaining widespread support, culminating in a confrontation with the government that tests the resolve of Huntly, Smudger, and their allies. The resolution highlights the impact of their efforts on society, offering a hopeful yet open-ended conclusion that underscores the importance of standing up against injustice. Through its engaging plot and relatable characters, "Chocolate Underground" presents a thought-provoking exploration of resistance and the enduring appeal of forbidden pleasures in a repressive society.