Stone Ocean

Set near Port St. Lucie, Florida in 2011, the story follows Jotaro Kujo's daughter, Jolyne Cujoh, who is framed for a murder and ends up in Green Dolphin Street Jail. Jotaro soon comes to visit her and informs her that a disciple of DIO's framed her so that he could kill her in prison, and urges her to escape. This plan goes awry when a Stand named Whitesnake uses its power to remove Jotaro's Stand and memories, in the form of discs. Jotaro sinks into a deathlike state, and Jolyne must find a way to recover the discs from Whitesnake's user, the mysterious prison chaplain Enrico Pucci. Along the way, she picks up allies such as Emporio Alniño, a boy born in the prison, Ermes Costello, and Narciso Anasui, who soon falls into unrequited love for Jolyne. Most notable of her allies is Weather Report, an amnesiac who can control the weather. She also meets Foo Fighters (shortened to F.F.), a mass of plankton that had been made sentient via Whitesnake and assumed the human appearance of a recently-deceased female inmate, who later dies at the hands of Pucci.

Pucci met and idolized DIO sometime before the events of Part 3 occurred. While in DIO's company, DIO spoke of "Heaven" and how to create a "perfect world" when certain conditions were met. Pucci, keeping DIO to his word, proceeds with his plan to realize this "perfect world", which involves absorbing the remnants of DIO's bones in the form of a green homunculus and arriving at a predestined place on the night of the new moon.

Jolyne, Ermes, and Emporio escape from prison on their hunt for Pucci while Anasui and Weather Report also escape in pursuit of Jolyne. She succeeds in sending both of Jotaro's discs to the Speedwagon Foundation. During a battle, Weather's memory disc is returned to him, after which he remembers his true name, Wes Bluemarine, that Pucci is in fact his long-lost twin brother, and the torment he went through before his memories were taken. With his memories returned, Weather unleashes his Stand's true powers and faces Pucci in combat. Weather Report is killed, and Pucci continues on to Cape Canaveral in time for the new moon.

Jolyne and company catch up to Pucci but all seems lost when they are faced by his evolved Stand, C-Moon. Jotaro arrives just in time and defends Jolyne and her friends from Pucci. However, Pucci realizes he can use C-Moon to replicate the gravitational conditions required for his plan. Unlocking his ultimate stand, Made in Heaven, Pucci speeds up time itself causing the rapid acceleration of the world around Pucci and the Joestar group. Made in Heaven greatly shortens Jotaro’s time stop, and while Jotaro is able to momentarily save Jolyne from Pucci's attack, he is killed along with Ermes and Anasui. Jolyne then sacrifices herself to halt Pucci and save Emporio.

The effects of Made in Heaven are completed when time accelerates to the end of the universe, leading to a new cycle of time and a parallel universe, where all surviving humans have precognitive understanding of fated actions in their lives; all deceased humans became different, but similar versions of themselves. Pucci, who believed that such knowledge of one's fate would bring all people happiness, proceeds to hunt down Emporio to ensure that the future does not change. As he is about to kill Emporio, he inadvertently changes fate when Made in Heaven pushes Weather Report's Stand Disc into Emporio’s head. Although Pucci accelerates time once more, Emporio is able to use Weather Report to increase the amount of oxygen in the room and kill Pucci.

In a universe without the precognitive effects of Pucci's, Emporio meets a young woman who looks identical to Ermes, and a couple in a car who look similar to Jolyne and Anasui, who introduce themselves as Irene and Anakiss. They offer the pair a ride as they head to see Irene's father. The group stops to pick up another hitchhiker, who bears a striking resemblance to Weather Report, as they drive off in the rain.

• Jolyne Cujoh[lower-alpha 2] is an inmate at Green Dolphin Street Jail, and is the daughter of the Stardust Crusaders main protagonist Jotaro Kujo. Her Stand is Stone Free,[lower-alpha 3] which allows her to unravel her body into elastic thread.
• Hermes Costello[lower-alpha 4] is an inmate who got her sentence on purpose, intending to get revenge on her sister's killer, Sports Maxx. She uses the Stand Kiss,[lower-alpha 5] which allows her to place stickers on objects that duplicate the objects perfectly until the sticker is removed, at which point the duplicate and the original will violently fuse together, leaving the object damaged.
• Foo Fighters,[lower-alpha 6] shortened to F.F., is a sapient being consisting of plankton, and is its own Stand.
• Emporio Alniño[lower-alpha 7] is a boy born to an unknown inmate in Green Dolphin Street Jail. His Stand, Burning Down the House,[lower-alpha 8] manifests in the form of a ghost room that he secretly lives in, together with Weather Report and Narciso Anasui.
• Weather Report[lower-alpha 9] is an amnesic inmate who aides Jolyne at Emporio's request. His Stand, also named Weather Report, allows him to manipulate the weather and the atmosphere.
• Narciso Anasui[lower-alpha 10] is an inmate who is in love with Jolyne, and wishes to marry her despite her clearly not being interested in him. His stand, Diver Down,[lower-alpha 11] allows him to phase himself or his Stand into objects, or into others' bodies to absorb damage dealt to them.
• Jotaro Kujo[lower-alpha 12] returns from Stardust Crusaders and Diamond is Unbreakable as Jolyne’s father. Now a middle-aged man, he arrives at Green Dolphin Street Jail to help Jolyne clear her name and stop Enrico Pucci. His stand is Star Platinum,[lower-alpha 13] a powerful close ranged Stand with immense strength, precision, speed, and the ability to stop time.
• Father Enrico Pucci[lower-alpha 14] is a Roman Catholic priest and Jolyne’s warden of the Green Dolphin Street Jail, and is one of the last loyalists to DIO. Pucci uses the Stand Whitesnake,[lower-alpha 15] which allows him to torture his prisoners to their breaking point by extracting their memories and Stands in the form of compact discs; he can then insert these disks into their bystanders for information about their crimes against the public so that he may mercilessly crucify his prisoners without trial. Whitesnake eventually evolves into C-Moon,[lower-alpha 16] giving Pucci the ability to reverse the gravity of the area around him, as well as the gravity of anything the Stand touches. After evolving once more, C-Moon changes into Made in Heaven,[lower-alpha 17] gaining the power to gradually speed up time until reaching a new parallel universe. In reality, Pucci seeks to avenge DIO and continue his plans by wiping out Jolyne and her family line of Joestars, and therefore rewriting reality into DIO's image.

Kono Manga ga Sugoi! recommended the series, and called Jolyne a distinctive character within the JoJo's Bizarre Adventure franchise.[30] In a 2015 poll on Charapedia, Japanese readers ranked Stone Ocean as having the seventeenth most shocking ending of all time in manga and anime.[31]