Chapter 1:
The story begins in the year 1988, in Egypt. Jotaro Kujo battles the invincible vampire DIO, newly empowered by the blood of the late Joseph Joestar. Though DIO blinds Jotaro with his own blood, Jotaro shatters DIO's Stand, The World, destroying the vampire's head and putting a definite end to his menace. The following night, Jotaro discovers and burns a diary left behind by DIO, fearing a deeper meaning behind its contents. The three survivors (including Joseph, revived via a blood transfusion from DIO's corpse) make their way to the city's airport, where Polnareff parts ways with the two Joestars to return to his home country of France. As Jotaro and Joseph turn to begin their own trip home to Japan, they are suddenly stopped by a young Robert E. O. Speedwagon. At the same time, Jean Pierre Polnareff rushes to their side, claiming to have been attacked on the plane before takeoff. The three subsequently encounter the thought-to-be-deceased Muhammad Avdol and Iggy, who meet the group with hostility, claiming that they were sent by "him."
The combatants leave the airport to avoid endangering civilians and, after a battle on the rooftops of Cairo, the two assailants are incapacitated. Immediately afterwards, the group is attacked by Noriaki Kakyoin and N'Doul, who were also thought to have died. After they are both defeated, N'Doul manages to escape, but Speedwagon uses a part of a mysterious Saint's Corpse to restore Kakyoin's sanity. Speedwagon explains that the Saint's Corpse Part in his possession has led him through time in search of an unknown danger that is causing strange phenomena and slowly destroying the space-time continuum. The Joestar Group agrees to help the Englishman gather the remaining eight parts of the Saint's Corpse. The group quickly finds the Corpse's torso nearby, which is entrusted to Jotaro for safekeeping. Speedwagon then guides the heroes through a light rift, a passage filled with light that connects time periods and dimensions.
Chapter 2:
Jotaro and Speedwagon appear at the Colosseum in Italy, 2001, where Guido Mista, Trish Una, and Giorno Giovanna have just defeated Diavolo. However, after Mista and Trish suddenly disappear, Giorno is attacked by Bruno Bucciarati, whose body and soul were both killed in the battle with Diavolo. Though Bucciarati is quickly fended off when Jotaro arrives on the scene, he and Giorno are then challenged by Narancia Ghirga and Pannacotta Fugo. Fugo disappears after his defeat, but Jotaro is able to restore Narancia using the Corpse's torso. Giorno's group and Jotaro trail Bucciarati to the Naples Train Station, where they meet with their allies. Bucciarati ambuses the group alongside Vanilla Ice, who Polnareff is certain was disintegrated by the sun's light. Both assassins escape, but Giorno finds and secures the Corpse's head. With Bucciarati gone, Trish and Mista free themselves from Sticky Fingers's zippers as the group prepares to enter another light rift, using Coco Jumbo's Stand to avoid being scattered when crossing through the rifts. What remains of Team Bucciarati recognizes Polnareff as the man in the turtle, but their reactions only confuse the Frenchman further. As the heroes enter the rift, a revived Diavolo watches from afar, having entered the service of "that man."
Chapter 3:
Jotaro and Joseph arrive at Morioh in the year 1999. Joseph recognizes the town, but quickly changes the subject and walks off when Jotaro questions him. Soon after, Josuke Higashikata and Koichi Hirose find Jotaro, but are soon attacked by Okuyasu Nijimura and Rohan Kishibe. After their defeat, Jotaro uses Star Platinum's time stop to prevent Rohan from escaping and successfully restores him. Okuyasu escapes, despite Josuke's best efforts to give chase. The group later converges at Boyoyoing Cape, where Josuke glimpses a group of Harvest's units and attempts to gather the rest, remembering the death of their user Shigekiyo Yangu at the hands of Yoshikage Kira. One group escapes and returns to Shigechi, who confronts Josuke and Jotaro alongside Akira Otoishi. After being defeated, both enemies escape. Jotaro finally forces Joseph to explain his relation to a confused Josuke inside Mr.President. Rohan and Koichi join Jotaro, but Yukako Yamagishi attacks the two, only to be defeated and disappear like the other enemies. Jotaro is suddenly confronted by Enya the Hag, who sends a group of corpses under her control to attack the group. Though the puppeteered corpses are defeated, Enya extols "his" virtues and "his" power to "overwrite" his enemies before disappearing. With the coast clear, Jotaro finds the Corpse's left arm and entrusts Josuke with it. Joseph then emerges from the turtle, revealing a camera he found inside. Via Joseph's Hermit Purple, the group finally glimpses their true enemy: the photo reveals none other than DIO himself, despite his certain death at Jotaro's hands.
Chapter 4:
The heroes' next stop is inside the Joestar Mansion in 1889. Speedwagon reveals that the mansion had suddenly reappeared after Jonathan Joestar's battle with Dio Brando, teeming with zombies. Jonathan took it upon himself to fight off the horde of zombies, but asked Speedwagon to find allies to aid their struggle. Jotaro and Speedwagon find a wounded Jonathan, as well as the era's Dio. The two Joestars fight through the horde, forcing Dio to take matters into his own hands—all four of them, as he has struck an uneasy alliance with Diego Brando. With Jonathan temporarily unable to fight, Jotaro and Speedwagon defeat the two Dios, who swear revenge as they flee. Jonathan recovers, but he and Jotaro are confronted by Mariah and Will A. Zeppeli, the latter having been revived and corrupted by the strange phenomenon. Jonathan and Jotaro manage to defeat Zeppeli and Mariah, who escape. As Jonathan collapses from exhaustion, Speedwagon returns the Corpse's eyes to him and accompanies him into the turtle.
Chapter 5:
Jotaro and Joseph arrive at Air Supplena Island in 1939, where the two meet Caesar Anthonio Zeppeli training alongside Joseph's younger self. Suddenly, Lisa Lisa and Rudol von Stroheim assault the two Ripple users. Stroheim flees after his defeat, but Jotaro succeeds in restoring Lisa Lisa, though she remains unconscious. As Caesar takes his master inside to rest, the two Josephs become acquainted with each other, despite the younger's disbelief in the group's time traveling abilities. Hol Horse then confronts Jotaro in search of the Saint's Corpse, but is defeated and disappears. As the younger Joseph explains the situation to Caesar, Esidisi, Wamuu and Kars suddenly appear, having tracked down the Red Stone of Aja. Despite sending vampires after Joseph and Caesar, Kars is eventually forced to grant Esidisi and Wamuu permission to battle the two Ripple users. The two heroes manage to overcome not only Esidisi and Wamuu, but Kars as well, though their Ripple is unable to destroy the Pillar Men. Lisa Lisa appears and announces her intent to fight off the Pillar Men, despite both Josephs knowing that she has not yet fully recovered. Despite Lisa Lisa's courage and Caesar's yearning to take revenge for his and Joseph's ancestors, the older Joseph calms the team and successfully bluffs Kars by claiming that the Red Stone of Aja is protected by a time bomb. The Pillar Men give Joseph and Caesar six days to prepare for their final battle before departing. The older Joseph then brings the group inside the turtle, where he explains the situation fully. Jotaro recovers the Corpse's ears and gives them to the younger Joseph.
Chapter 6:
The first thing Jotaro notices is the floor to his left: he has arrived in 2011 at Kennedy Space Center, currently under the influence of C-MOON's gravitational pull. Jotaro then spots Jolyne Cujoh and Emporio Alnino, who believe Ermes Costello and Narciso Anasui's betrayal of the two to be part of Enrico Pucci's newfound power. The two are both relieved upon seeing Jotaro alive and well, but Jolyne is caught off guard by his younger age. Jotaro joins Jolyne in fighting Ermes and Anasui, and manages to restore both. Anasui becomes jealous of Jotaro's proximity to Jolyne until she properly introduces her father, surprising even Jotaro himself. Sick of explanations by this point, Jotaro orders Ermes, Anasui and Emporio into the turtle to hear the older Joseph's explanation. Before Jolyne can join them, she and Jotaro are attacked by a phenomenon-possessed Weather Report, who escapes following his defeat. Finally, Pucci himself appears before Jotaro and Jolyne, accompanied by Pet Shop. Pucci explains that "his friend" has shown him a greater truth than the path to Heaven he once sought, and that it is this truth he now strives to achieve. Despite Pucci's unsuccessful attack on the father-daughter duo, he announces his intent to guide the people of the world to eternal bliss through the true path to Heaven, which he dubs the "Eyes of Heaven." As he and Pet Shop depart, Pucci warns Jotaro that, once his group gathers the entire Saint's Corpse, "his friend" will draw open the curtains to Heaven himself.
After finding the Corpse's right arm and entrusting it to Jolyne, the group returns to Morioh to receive Rohan's report on the mysterious phenomena, unaware that Funny Valentine has witnessed the battle from afar. When Jotaro finds himself unable to exit Morioh through the light rift, Speedwagon observes that the rift is only permitting certain individuals to pass through it. At that moment, Jonathan and Josuke's Corpse parts resonate, revealing them to be the individuals currently permitted into the rift. As the rest of the group stays behind in Morioh, Jolyne decides to go for a walk and soon stumbles into a gambler at Morioh's Cafe Deux Magots. The gambler coerces Jolyne into betting her soul on a coin flip; just as Jotaro recognizes the gambler as his old foe Daniel J. D'Arby, Jolyne loses the bet and has her soul taken by Osiris. Jotaro then examines D'Arby's coin, which, naturally, has tails on both sides. Determined not to be humiliated again, D'Arby has come independently of "his" orders to challenge Jotaro to a poker game, with both his and Jolyne's souls on the line. Jotaro comes out on top, and D'Arby is forced to return Jolyne's soul to her body. Before disappearing, D'Arby warns Jotaro that "his" power is not to be trifled with. Jotaro deduces from Enya and Pucci's earlier clues that the true enemy's power has something to do with "overwriting the truth."
Chapter 7:
Jonathan finds himself alone on the Philadelphia Coastline in the 1890 of an alternate timeline. Jonathan notices Johnny Joestar near the Corpse's legs, awaiting Funny Valentine's return and final attack. Valentine appears before Johnny, but reveals that the infinite rotation placed upon him by Tusk has disappeared completely. Valentine explains that someone has interrupted their fight, and asks the two Jonathans to continue gathering the Saint's Corpse, warning that the true battle will begin once the Corpse is gathered. Johnny then notices that the Corpse's legs have disappeared. Though Jonathan uses his Ripple to heal Slow Dancer's wounded leg, Johnny accuses the Englishman of stealing the Corpse part, but calms down when Jonathan shows him his own part of the Corpse. After hearing Jonathan's explanation, Johnny agrees to help Jonathan, as they share the goal of collecting the completed Saint's Corpse.
The two depart through the light rift to a village in the Rocky Mountains, where they are forced to hide from a prowling dinosaur. Johnny is bewildered, having seen Diego die with his own two eyes. Diego himself soon appears and commands the dinosaurs to attack the two Jonathans, who handily defend themselves against the pack. Dio joins Diego once more, declaring that he himself will be the one to kill Jonathan; Diego offers no objection, holding a grudge himself against Johnny. The two Dios are defeated and leave, but Valentine suddenly reappears alongside a phenomenon-possessed Gyro Zeppeli. Despite Johnny's refusal to believe what he sees, Valentine urges the jockey to fight him and demonstrate his Stand's full potential. The two Joestars emerge victorious, but Gyro escapes before they can restore him. Valentine praises Johnny's potential, but notes that Giorno's power may also stand a chance against "him." As Valentine leaves, Jonathan finds the Corpse's legs, which are entrusted to Johnny. Johnny laments the loss of his closest friend, but Jonathan reassures him that, with the Corpse Parts, they may be able to fight off the strange phenomena and save Gyro.
Chapter 8:
Meanwhile, Josuke is sent to the Higashikata House in the alternate universe's Morioh of the year 2011. In the distance, Josuke overhears an argument between Joshu Higashikata and an amnesiac also named Josuke Higashikata. Josuke 8 suddenly sees an abnormal purple energy swirling behind Joshu, and the energy soon engulfs him. Recognizing the phenomena, Josuke 4 springs into action and attempts to explain the situation to Josuke 8. Joshu stands up, the corruption only fueling his resentment, but the two Josukes quickly defeat him despite their mutual lack of familiarity with Joshu's Nut King Call. Josuke 4 restores Joshu with his Saint's Corpse Part, but knocks him down again when he becomes confrontational, excusing his actions to the other Josuke by claiming that the restoration hadn't taken effect yet. Josuke 8 recognizes the Corpse part, which aids Josuke 4 in his explanation. Josuke 8 agrees to lend his help, but Josuke 4 feels as though the two are being watched. Their "pursuers" reveal themselves as two versions of the original timeline's Yoshikage Kira, the latter impersonating Kosaku Kawajiri. The two Kiras reveal that they had come on their own seeking peaceful lives, resenting Josuke's sudden reappearance. The Josukes fight and triumph over the Kiras, who disappear in disappointment. After they leave, Joshu wakes up, unable to remember what happened. Josuke 4 finds the Corpse's heart nearby and gives it to Josuke 8. Before the two Josukes return to Morioh, Joshu decides that he also wants to tag along.
Chapter 9:
Back in the original universe's Morioh, Jonathan reappears with Johnny, shortly followed by Josuke 4, Josuke 8, and Joshu. Speedwagon then assembles the Joestars to review their progress. Realizing that the final part of the Corpse is missing, the group ponders its location. Suddenly, Enya reappears and taunts the Joestars, proclaiming that "he" has already seized the Corpse's spine. Though she is defeated once again, Enya triumphantly announces to the heavens that the Joestars have collected eight parts of the Saint's Corpse before disappearing. Suddenly, everything begins to tremble as the reality around the group disappears into a celestial ocean. A figure approaches the group, proclaiming that their Corpse parts have reacted to the Corpse's spine and brought them to "the foundation of the world." The one speaking to them finally reveals himself: it is none other than DIO, though he bears a radically different appearance from his 1988 counterpart.
Johnny charges forward, hoping that defeating DIO will bring Gyro back, but DIO's new Stand, The World Over Heaven, easily repels his attack. Before DIO can counterattack, Giorno blocks with Gold Experience Requiem, but finds it has no effect on DIO; Jotaro lands a blow with Star Platinum, but by simply placing a hand over the wound DIO heals it completely. The World Over Heaven pummels Johnny, Jotaro and Giorno, knocking all three away. DIO then uses the Corpse's spine to draw the other Corpse Parts to him, absorbing them into himself and amplifying his power even further. Before DIO can eliminate the Joestars, however, light rifts appear at their feet. As his enemies escape, DIO realizes that he is missing one Corpse part: the torso, which remains in Jotaro's possession. DIO, declaring Jotaro his greatest threat and the Joestar Family's last hope, asks Enya to give the Corpse parts to his underlings and have them pursue Jotaro's group. As Enya sets out, DIO looks forward to his possession of the completed Saint's Corpse and the total extinction of the Joestar family.
Chapter 10:
The Joestars escape to Air Supplena Island, in disbelief that even Johnny and Giorno's infinite abilities stood no chance against DIO. Suddenly, Valentine reappears and challenges Jotaro to a fight, hoping to witness the power of Star Platinum. By doing so, Valentine realizes that Star Platinum and The World are the same type of Stand, even after their evolution, explaining why DIO was unable to take Jotaro's part of the Corpse. Valentine explains his story to the group: his initial goal was to gather the Saint's Corpse, but after Johnny attacked him with the infinite rotation, he was forced to use Dirty Deeds Done Dirt Cheap to escape through several parallel worlds. In one of these, Valentine found, DIO succeeded in defeating the Joestars and evolving his Stand to its full potential, conquering reality itself. Realizing that the world he ruled was only one of many, DIO decided to invade the original universe and conquer it. Valentine finally confesses that he wishes to defeat DIO, who poses a direct threat to his country; he merely pretended to be loyal to DIO while seeking someone who could defeat him. Even Valentine himself is unaware of the secret behind The World Over Heaven's power, which he believes is the key to allowing Jotaro to defeat him. Valentine concludes by demonstrating that two objects from different dimensions cannot coexist, being forced to violently merge together and disappear; though the DIO of this timeline is defeated, Valentine reminds Jotaro about the vampire's remains before he departs.
Though Johnny continues to distrust Valentine, the Joestars reaffirm their will to fight DIO. Jotaro finds four good reasons to continue fighting: to retrieve the Saint's Corpse, to bring back the allies DIO has been manipulating, to find out the secret to DIO's ability... and because he is getting tired of DIO. Despite the odds being turned against them, the group successfully recovers four of the Corpse parts they have lost and restore Okuyasu, Stroheim, Will and Gyro Zeppeli, Bucciarati, and Yukako. Jotaro recovers one of the parts from D'Arby, who also reveals that DIO requires souls to complete his Stand's true ability, of which Pucci alone knows. Jotaro then returns to the Cairo of 1988, where finds the bracelets of the original universe's DIO. Remembering Valentine's advice, Jotaro takes the bracelets in hopes that they might prove useful.
Meanwhile, at the Joestar Mansion, Pucci informs DIO of the Joestar group's progress. DIO remains confident, however, believing that the Corpse parts are simply a means to an end. What is truly important, DIO states, are the 36 sinners' souls he seeks. The "criminals" who turned their backs on Heaven are influenced by the Joestar bloodline, and may eventually stand against him; thus, DIO must absorb these sinners' souls to achieve his ambition of conquering the world. Pucci then informs DIO that Valentine is among the sinners, and DIO promises to deal with him. As DIO begins to leave, Pucci asks him to let him defeat those whose souls are not worth sacrificing, which DIO grants. Now alone in the mansion, Pucci prays for deliverance from those who would hinder his and DIO's way to Heaven.
Chapter 11:
The Joestar group continues collecting the remaining pieces of the Corpse. At Boyoyoing Cape, Josuke 4 and Okuyasu defeat and restore Shigechi and Otoishi, and Jotaro collects the Corpse's head. The group then visits the Colosseum, where Diavolo challenges Giorno in order to retain his pride as an emperor. After the former boss is defeated, he surrenders the Corpse's legs and departs. The group defeats Dio and Diego once more at Air Supplena Island before finally battling and restoring Avdol and Iggy. Meanwhile, Valentine emerges in Cairo. Despite the president desperately fleeing through multiple parallel worlds, DIO effortlessly appears before Valentine and confronts him regarding his plans. Valentine declares that all of his actions have been in the name of justice before engaging DIO, who simply uses The World Over Heaven to erase him from existence. Jotaro and Jolyne follow the last Corpse part to the Joestar Mansion, where Pucci awaits him. Pucci, aware of what Jotaro is about to ask, states that there is nothing they can do against DIO's power, and that those foolish enough to oppose him will face Heaven's judgement. The priest sends a horde of zombies after the two, but they are quickly wiped out.
The priest, preparing to face the Kujos directly, praises their location as a place of destiny, the place where DIO's path to Heaven began. Pucci claims that DIO has shown him his destiny: a higher path to Heaven to walk on and to guide people toward, which he will demonstrate to those before him now. Pucci sings the praises of the "Eyes of Heaven," the salvation of mankind. Jotaro and Jolyne engage in battle with the priest, eventually defeating him completely. A defeated Pucci, knowing that the older Joseph can use Hermit Purple to extract DIO's secrets from his memories, moves toward the railing of the mansion's second floor. Indeed, Pucci feels a strange tranquility, as DIO draws closer to his ultimate goal: the souls of the 36 sinners he requires are none other than those of the expanded Joestar group. Under normal conditions, a person can only bear one soul; Pucci admits to wondering what would happen if one could absorb the power of multiple souls, and to having wanted to witness the heights DIO would reach. Declaring his love for DIO one final time, Pucci throws himself from the second floor and impales himself on the Statue of the Goddess of Love, ending his life and preventing the group from uncovering DIO's weakness. Even with this setback, Jotaro retrieves the eyes of the Saint's Corpse.
Chapter 12:
The group finally returns to Egypt to confront DIO. Jotaro and Johnny face DIO in battle, where he demonstrates his power over space and time, including the power to turn his enemies against themselves. Despite all odds, the two seemingly defeat him, only for DIO to immediately heal his wounds. DIO additionally reveals that he discreetly marked Coco Jumbo with The World Over Heaven during the battle, thus obtaining power over all of those inside the turtle. As Jotaro and Jolyne stay behind to battle DIO once more, the other Joestars and Speedwagon use the light rifts to track down and restore their allies. However, Giorno realizes too late that DIO's true plan was to separate the Joestars and their allies from Jotaro and Jolyne, allowing him to overwrite the group and absorb their souls along with the complete Saint's Corpse. DIO, who now holds the power to rewrite the universe itself to his liking, strikes Jotaro decisively and proclaims his complete victory... and yet Jotaro remains standing. To the surprise of both DIO and Jolyne, Star Platinum has evolved into Star Platinum Over Heaven and countered DIO's ability, being the same type of Stand as DIO's; with their hope reinforced, the Kujos make one final stand against DIO.
Despite his defeat, DIO simply heals his wounds once more before killing Jolyne and absorbing her soul. DIO approaches a wounded Jotaro and prepares to finally make the Joestar family disappear for good. At the last moment, Jotaro remembers Valentine's advice and reveals the original DIO's bracelets, which fuse with Heaven Ascension DIO's bracelets and destroy his hands, putting The World Over Heaven's ability out of commission. Though DIO blinds Jotaro with his own blood, Jotaro finishes DIO with one final barrage, destroying him completely and putting a definite end to his menace. The souls DIO has absorbed leave his body as Jotaro's view is engulfed by light.
Jotaro finds himself in Cairo, at the moment after he burned DIO's diary. Joseph and Polnareff catch up to him, informing him that Avdol, Iggy, and Kakyoin are resting in the hospital. The three make their way to the city's airport, where Polnareff parts ways with the two Joestars to stay behind and take care of his friends. As they leave for Japan, Jotaro and Joseph promise to return to Egypt one day once their friends fully recover. As the game draws to a close, it is revealed that the Joestars and their friends in other eras have survived as well, a brighter timeline having come about despite all of the hardships they have faced.
In the year 1999, Koichi encounters an incredibly tall man in his home town of Morioh, accompanied by his young daughter. The man had decided to bring her along, supposedly because she refused to stop crying until he caved in. After the girl runs off to look at a turtle, the tall man asks Koichi about the location of a certain Josuke Higashikata...
