"JoJo's Bizarre Adventure: Stone Ocean" is the fifth part of the "JoJo's Bizarre Adventure" series, adapting Hirohiko Araki's manga of the same name. Set in 2011, the story takes place primarily in Green Dolphin Street Prison, a high-security correctional facility in Florida. The protagonist, Jolyne Cujoh, is the daughter of Jotaro Kujo, a recurring character from previous arcs. Jolyne is wrongfully imprisoned after being framed for a hit-and-run incident orchestrated by an enigmatic figure. While incarcerated, she discovers a mysterious pendant given to her by her father, which awakens her Stand ability, Stone Free. Stands are manifestations of a person's fighting spirit, each with unique powers.

Jolyne's goal is to uncover the truth behind her imprisonment and protect her father, who is targeted by the series' overarching antagonist, Enrico Pucci, a priest with a deep connection to the late Dio Brando. Pucci seeks to achieve a divine plan involving the manipulation of fate and the universe itself, using a Stand named Whitesnake, which can extract and manipulate memories and Stand abilities. Jolyne forms alliances with fellow inmates, including Ermes Costello, whose Stand, Kiss, allows her to create and manipulate stickers that duplicate objects, and Foo Fighters, a sentient colony of plankton inhabiting a human body, capable of healing and controlling water.

As the story progresses, Jolyne and her allies face numerous Stand users within the prison, each with abilities that challenge their ingenuity and resolve. The narrative explores themes of fate, free will, and the consequences of one's actions, as Jolyne uncovers Pucci's plan to use a mysterious artifact known as the "Green Baby" to achieve his goals. The Green Baby is a key element in Pucci's scheme to reset the universe, aligning it with Dio's vision of absolute control.

The climax of the story involves a high-stakes battle against Pucci, who evolves his Stand into Made in Heaven, granting him the power to accelerate time and rewrite reality. Jolyne and her allies fight to prevent the universe's reset, leading to a dramatic and emotionally charged conclusion. The arc concludes with significant consequences for the characters and the broader "JoJo's Bizarre Adventure" universe, setting the stage for future developments in the series.