Chapter 1:
The story begins with the final battle between Jotaro Kujo and DIO in Egypt, 1988, as Jotaro defeats DIO as per the original storyline and burns his diary the following night. On their way back to Japan, Jotaro and Joseph Joestar are stopped by a young Robert E. O. Speedwagon at the airport shortly before Jean Pierre Polnareff returns to them, 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". They flee the airport to avoid endangering civilians and, after a battle on the rooftops of Cairo, the two assailants are incapacitated. Immediately afterwards, Jotaro, Polnareff and Joseph are attacked by Noriaki Kakyoin and N'Doul, who were also thought to have been dead. After they are both defeated, N'Doul manages to escape, but Speedwagon uses a part of the Saint's Corpse he obtained beforehand to heal Kakyoin. 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, like bringing people back from the dead; thus, supposedly slowly destroying the time-space continuum. Speedwagon then enlists the Crusaders' help in gathering the remaining eight parts of the Saint's Corpse, just as the one in his possession resonates, indicating another part nearby. The part is found and kept by Jotaro, and Speedwagon guides the heroes through a "light rift", a dimensional crack from which light seeps out, where they travel to another time period to continue their search.
Chapter 2:
A brief summary of the events of Vento Aureo is shown as Jotaro and Speedwagon appear at the Colosseum in 2001, where Guido Mista, Trish Una and Giorno Giovanna reside, having defeated Diavolo. After Mista and Trish suddenly disappear, Giorno is attacked by Bruno Bucciarati, who was originally supposed to be dead. Bucciarati is quickly fended off after Jotaro arrives at the scene and the two are then challenged by Narancia Ghirga and Pannacotta Fugo. After their defeat, Fugo disappears, but Jotaro is able to heal Narancia using the life energy of his Saint's Corpse part and brings him to their side. Jotaro and Giorno head to the Napoli Train Station where they find Polnareff; Giorno feels like he knows Polnareff from somewhere but cannot remember. Bucciarati appears once again with Vanilla Ice and after a brief bout, the two escape. Soon after Giorno finds and secures the third Saint's Corpse Part, Trish and Mista, who had been trapped by Bucciarati's Sticky Fingers when Giorno was not looking (thus explaining their disappearance), appear with Narancia and they recognize who Polnareff is, claiming that he is "Polnareff the Turtle" (by that time, the older Polnareff's soul was inhabiting Coco Jumbo's body). Polnareff is confused by this, so the group decides to it's best to pretend they don't know him. Speedwagon takes them inside Mr.President so the ever-growing group can cross over the light rifts without overloading them, which is done by way of Jotaro tucking Coco Jumbo into his jacket. Unknown to the heroes, they are spied on by a revived Diavolo, who is currently working for "that man".
Chapter 3:
Jotaro and Joseph arrive at Morioh in 1999. Joseph recognizes the town, but quickly changes the subject and walks off when Jotaro asks him about it. Soon after, Josuke Higashikata and Koichi Hirose find Jotaro, who asks them about strange happenings in town. As Koichi thinks about what to tell him, Okuyasu Nijimura and Rohan Kishibe appear and attack them for interfering with "his" plans, forcing Josuke and Koichi to battle them. After their defeat, Okuyasu and Rohan try to escape, but Jotaro uses Star Platinum's time stop ability to stop them in their tracks and heal them with his part of the Saint's Corpse. While Rohan is successfully healed, Okuyasu escapes and Josuke gives chase. Later, Jotaro finds Joseph and explains to him that they are ten years into their future, when Josuke appears, saying he trailed Okuyasu until he disappeared. After learning he is talking to a younger Jotaro, Josuke spots one of Harvest's beings and chases after it to gather them, having remembered that Shigechi died at the hands of Yoshikage Kira. One of them, however, escapes and returns to Shigechi who, joined by Akira Otoishi, confronts Josuke and Jotaro. After being defeated, Shigechi and Otoishi escape, and Jotaro asks Joseph to explain the situation to a very nervous Josuke. For obvious reasons, Joseph keeps trying to dodge it, until Jotaro forces him to do so by having them enter Mr.President. Rohan and Koichi soon join Jotaro, when Yukako Yamagishi appears, under the influence of a strange phenomenon and ready to fight them. After being defeated, Yukako disappears like the rest. Unexpectedly, Enya the Hag shows up and sends her zombies to attack Jotaro, Rohan and Koichi. After the zombies are defeated, Enya extols "his" virtues and "his" power to "overwrite" and leaves. Jotaro then convinces Rohan and Koichi to help him search for the Saint's Corpse Parts. As Josuke returns, Jotaro's Corpse Part starts resonating, and the fourth Corpse Part is given to Josuke for safekeeping. Joseph then reappears, showing a camera he found in Mr.President and, using Hermit Purple on it, a picture of a white-skinned DIO is developed - much to the Crusaders' shock, as they were assured of DIO's demise at Jotaro's hands.
Chapter 4:
The heroes' next stop is inside the Joestar Mansion, in 19th century England. Jotaro and Speedwagon arrive in this century as Speedwagon realizes that the Joestar Mansion was supposed to be destroyed from their previous battle with Dio Brando. They soon find a badly battered Jonathan Joestar, followed by the era's Dio, who commands his zombies to fight his opponents. Jonathan, helped by Jotaro, makes short work of them, and Dio, interested in Jotaro's Stand powers, decides to take matters into his own hands, joined by Diego Brando. Despite the animosity between them, they decide to team up to eliminate Jonathan (whom Diego recognizes as Johnny's counterpart), but Speedwagon takes his friend's place to fight them with Jotaro. When Dio and Diego are defeated, they flee, swearing revenge. Speedwagon then tells Jotaro about the first strange phenomenon they sensed: just after finding out Dio was hiding in Windknight's Lot, the Joestar Mansion, which had been burned to the ground, suddenly reappeared, infested with zombies: that was when Jonathan and Speedwagon found the first Saint's Corpse Part, and Jonathan stayed behind to secure the mansion. Speedwagon wanted to help, but was forcibly sent to retrieve the rest of the Saint's Corpse Parts. While a recovered Jonathan and Jotaro get acquainted, Mariah appears, shortly followed by Will Zeppeli, who is revived and now under the influence of the era's strange phenomenon. Jonathan sees no other choice than to fight his master, despite not being completely recovered. Still, he and Jotaro manage to defeat Zeppeli and Mariah, who escape. Speedwagon passes his Saint's Corpse Part on to Jonathan, who then collapses due to exhaustion. Speedwagon brings him to Mr.President so he can rest.
Chapter 5:
Jotaro arrives at Air Supplena Island along with Joseph, who tells him about the island and how they hope to get helpful information there. Upon seeing Caesar Zeppeli, along with his younger self, Joseph realizes they had gone back to 1938. Caesar and the young Joseph meet Jotaro and the old Joseph with some mistrust, when Lisa Lisa appears and attacks Caesar. Rudol von Stroheim appears afterwards, under the influence of a strange phenomenon like Lisa Lisa, and tells Joseph that "his" power brought him back to life, more powerful than before. Joseph decides to fight them, along with a hesitant Caesar. After they are defeated, Stroheim flees, but Lisa Lisa, left barely conscious, is brought back to normal by Jotaro. As Caesar takes her inside to rest, the young Joseph, still not knowing he is talking to his older self, manages to sense his Ripple by touching his shoulder. The old Joseph is reluctant to tell his younger self that they are one and the same, but Jotaro practically forces him to come clean. Joseph tells his younger self that they are traveling through time, and has the younger Speedwagon from the 19th century come out to prove his point. As the young Joseph recovers from the shock of these revelations, Jotaro senses someone else coming: it is Hol Horse, who confronts Jotaro for the Saint's Corpse Parts. He is, however, defeated, and after withholding information on "him" when asked by Jotaro, disappears like the others, before Caesar comes out, incensed. The younger Joseph tries to calm him down by making up a story about them being acquaintances of his when, suddenly, Esidisi, Wamuu and Kars appear, having trailed the Red Stone of Aja to an island next to Air Supplena and had made a stopgap. Wamuu asks if he can have his promised rematch with Joseph, but Kars instead sends vampires to attack the heroes. With the vampires defeated, Kars allows Wamuu to fight Joseph and sends Esidisi along with him, so the young Joseph and Caesar fight them together. When they manage to prevail over the two Pillar Men, Kars decides to take matters into his hands and fights them in the others' stead, since their priority is still the Red Stone of Aja. Even though Kars has been defeated, the old Joseph recognizes that the power of their Ripple is still not enough to take out the Pillar Men, when Lisa Lisa, recovered, decides to fight off the Pillar Men. Both iterations of Joseph observe that she hasn't completely recovered and would be defeated for sure until the old Joseph tackles the situation by bluffing Kars with knowledge of the Red Stone of Aja. After a lengthy "team talk" in which the young Joseph nearly blurts out his older self's identity, the old Joseph convinces the Pillar Men to give Joseph and Caesar six days to prepare for their final battle. They leave, but not before Esidisi expresses his desire to test out the old Joseph's Ripple in battle. When Lisa Lisa asks for the old Joseph's identity, he convinces them all to enter Mr.President so he can explain himself better. Left alone, Jotaro senses another Saint's Corpse Part and lets the young Joseph out so he can safeguard it.
Chapter 6:
When Jotaro arrives, the first thing he notices is how the ground appears to be turned on its side: he is in the Cape Canaveral USAF Station after C-Moon used its powers to change the gravitational pull, in 2011. Looking further, he spots Jolyne Cujoh and Emporio Alniño talking about Enrico Pucci's newfound powers and how Jolyne is determined to not let Pucci get away from her when Jotaro approaches them. They are both relieved to see him alive and well, but Jolyne instantly realizes something's off when she sees her father looking about 20 years younger. Jotaro ponders about this, when they are approached by Ermes Costello and Narciso Anasui, who are affected by this age's strange phenomenon, and so Jotaro joins Jolyne in fighting them. After the fight, Jotaro manages to heal both Ermes and Anasui with his Saint's Corpse Part. When Anasui starts to get jealous of Jotaro, Jolyne ends up telling everyone he's her father, even though he is 20 years younger and has traveled from the past, surprising even the teenage Jotaro. Not wanting to bother with explanations, he asks Joseph, who by this point is starting to get annoyed, to get Jolyne and her friends up to speed. Ermes, Anasui and Emporio follow Joseph into Mr.President, but Jolyne stays behind long enough to spot a phenomenon-possessed Weather Report. Once he is defeated, he disappears, and Pucci comes out to confront 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 now he strives to achieve this truth; in order to do so, he must defeat Jotaro and Jolyne, body and soul. He, however, ends up defeated, but regardless explains that he has found the true path to Heaven and intends to guide the people of the world to eternal bliss through this path, which he calls the "Eyes of Heaven". As he and Pet Shop leave, Pucci warns Jotaro that once all of the Saint's Corpse Parts are gathered, that is when "his friend" will draw open the curtains to Heaven. Jotaro is left to think about how Pucci could be the cause of the strange phenomena, and what the "truth" he mentioned could be, as his Saint's Corpse Part starts resonating. The sixth Saint's Corpse Part is found and entrusted to Jolyne. While departing to Morioh, the heroes are unaware that Funny Valentine is watching them from the shadows. After taking a detour to 1999 Morioh to pick up a report of Rohan's notes on the phenomena, Jotaro finds himself unable to exit Morioh through the light rift. Speedwagon observes that the rift has built a protective wall around itself, and only someone "qualified" can get through. At that moment, one of the Saint's Corpse Parts resonates amongst all the JoJos assembled there, which is quickly revealed to be Josuke's, followed by Jonathan's, meaning they are the only ones who can cross the rift to the next era, while the rest stays at Morioh. Feeling a bit bothered, Jolyne decides to go for a walk, stopping at the Cafe Deux Magots, where she meets Daniel J. D'Arby, who tries to goad Jolyne into a wager. Observing that she has seen through his loaded deck, he tries a game of heads-or-tails. D'Arby then appears to digress by talking about Jolyne's star birthmark, until he mentions the "Eyes of Heaven" just as he tosses his coin, and it lands on tails, as he had called before. Jotaro arrives too late to warn Jolyne about D'Arby, as Osiris steals her soul immediately afterwards. Jotaro then finds out that D'Arby's coin is loaded, with tails on both faces. Determined not to be humiliated again, D'Arby challenges Jotaro to a poker game, with Jolyne's soul on the line; Jotaro ups the ante by wagering his own soul as well. As before, Jotaro manages to win by calling D'Arby's bluffs and eroding his composure, thus restoring Jolyne's soul to her. Before disappearing, D'Arby warns Jotaro that "his" power is not to be trifled with, but "he" will fight if confronted. Jotaro deduces that it has something to do with "overwriting the truth", having put together the hints that were dropped earlier by Enya and Pucci, and has a hunch of who could have such a power.
Chapter 7:
Jonathan finds himself alone in the 1890's U.S.A. of the alternate timeline, along a coastline. He looks around and sees Johnny Joestar, kneeling on the ground, next to a Saint's Corpse Part. As Jonathan tries to approach him, Valentine appears before Johnny, apparently unharmed after taking the full power of Johnny's Golden Rotation. Valentine explains that someone interrupted their fight and it went unfinished, then turns his attention to Jonathan. He tells him to continue gathering the Corpse Parts, and warns him that, when all are gathered, the true battle will start, before vanishing. Johnny then notices the Corpse Part that was next to him is gone, while Jonathan uses his Ripple to heal Slow Dancer's wounded leg. He then asks Johnny about the Parts, showing his own, when Johnny, in despair, almost accuses Jonathan of being a thief, before straightening out his thoughts and allowing Jonathan to tell him about the quest for the Saint's Corpse Parts and all that happened so far. Johnny accepts to help Jonathan because he, too, is searching for the Corpse Parts. They depart through the light rift to a village in the Rocky Mountains, where Johnny spots a prowling dinosaur (a villager transformed by Scary Monsters) and brings Jonathan into hiding with him. Johnny thinks it is weird, because he saw Diego dying at the New Jersey Railway. Jonathan tells Johnny that he had met Diego before, and Johnny deduces he is using the dinosaurs to look for the Saint's Corpse Parts. They decide to leave to gather the Corpse Parts, when Diego appears and summons his dinosaurs to stop the Joestars. They, however, manage to defeat the creatures, and Dio joins Diego, warning that he will be the one to take out Jonathan, as is his fate, while Diego takes it upon himself to deal with Johnny. After they are defeated and leave, Valentine reappears, bringing along a phenomenon-possessed Gyro Zeppeli. Johnny refuses to believe this, as Valentine goads him into powering his Stand up to the fullest. Johnny and Jonathan manage to defeat Gyro and Valentine, and Johnny's attempts to get to Gyro are in vain, as he escapes, still influenced by the phenomenon. Valentine then praises Johnny's potential, but tells them about Giorno's power, which is expected to be on par with "his". After he leaves, Jonathan's Saint's Corpse Part resonates, indicating the presence of another Corpse Part, which is entrusted to Johnny, who laments the losses in his life. Jonathan sympathizes with him, then tries to cheer him up by saying that, with the Corpse Parts, they may be able to fight off the strange phenomena and save his friends.
Chapter 8:
Josuke, in the meantime, is sent to the Higashikata Family Estate, in the Morioh of the alternate timeline, only noticing Jonathan is not with him after taking in his surroundings. In the distance, he spots Joshu Higashikata and the alternate Josuke Higashikata. Joshu is, as usual, whining how Josuke is always getting the best of him, until Josuke spots an abnormal purple energy swirling behind Joshu, which soon engulfs him. Knowing what this means, Josuke 4 decides to act fast. As he attempts to explain the situation to Josuke 8, Joshu stands up, the corruption fueling his resentment; Josuke 4 quickly joins Josuke 8 to take on him, and they defeat him handily, despite their mutual lack of familiarity with Joshu's own Stand, Nut King Call. Josuke 4 heals Joshu with his Saint's Corpse Part, but knocks him down again when he starts to get confrontational, thinking he hasn't been healed. Josuke 8 recognizes the Corpse Part, and Josuke 4 fills him in on their quest. Having seen the Saint's Corpse Part he had heard about, Josuke 8 agrees to lend his help, as Josuke 4 feels they are being watched. The one who was observing them reveals himself: it's Yoshikage Kira, joined by another Kira, this one impersonating Kosaku Kawajiri. The combined power of both Josukes manages to bring both Kiras down, and they disappear expressing their desire for a "peaceful life" and, as such, the Saint's Corpse Parts do not matter to them. After they leave, Joshu wakes up, not remembering what happened, but shocked all the same. Josuke 4's Saint's Corpse Part then starts resonating, indicating another Corpse Part nearby, which is found and entrusted to Josuke 8. When Josuke 8 accepts to join the quest for the Corpse Parts, Joshu also decides he wants to tag along.
Chapter 9:
At the prime universe Morioh, Speedwagon and Jotaro are waiting for Jonathan and Josuke 4 to return, the former worried about his friend. Jonathan reappears along with Johnny, shortly followed by Josuke 4, Josuke 8 and Joshu. Speedwagon then assembles the JoJos to review which Corpse Parts they have:
- Jonathan has the eyes;
- Young Joseph, the ears;
- Jotaro, the torso;
- Josuke 4, the left arm;
- Giorno, the head;
- Jolyne, the right arm;
- Johnny, the legs;
- and Josuke 8, the heart.
Speedwagon then wonders where the final Corpse Part could be. Giorno then remembers that, when Bucciarati and Fugo escaped, they were enveloped in lights similar to those of the Saint's Corpse Parts before disappearing, and wonders if there could be any connection. Suddenly, Enya appears, taunting the Joestars about how they will never find the final Corpse Part, the vertebral spine, which "he" has already seized. She says that they are destined to be slaughtered and have the Corpse Parts stolen away, but as "he" cannot be bothered with that, she will take it upon herself to eliminate them by attacking along with her zombies. Despite being outraged at her defeat, Enya says she has fulfilled her duties to investigate on them and leaves. Suddenly, everything starts trembling, and the reality around them gets distorted: the Joestars are all transported to some sort of celestial ocean. A figure approaches them, stating that the gathered Corpse Parts reacted with the Corpse's spine and sent them to that place, which he dubs "The Foundation of the World". Jotaro's hunch is confirmed as the one speaking to them is none other than DIO, looking much different than before, with pale white skin and longer hair. Johnny charges forward, hoping that defeating DIO will bring Gyro back, but DIO's significantly powered-up The World easily repels his attack with Tusk ACT4, but just before he can attack Johnny, Giorno has Gold Experience Requiem stop the attack and, while he is repelled, Jotaro lands a blow with Star Platinum. DIO uses his godlike healing factor to roll with the punch and knocks Johnny, Jotaro and Giorno away at the same time. DIO then uses the Saint's 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 they escape, DIO realizes there is still one part of the corpse missing - the one that Jotaro kept with himself. DIO is annoyed that, even in the universal interference world he created, he must be the one to deal with Jotaro, considering him as his greatest threat and the Joestar Group's last hope. He then asks Enya to give the Corpse Parts in his possession to his underlings so that they can pursue Jotaro and the others. Finally, DIO contemplates how, once he has the last Corpse Part in his possession, he will orchestrate the extinction of the Joestars with his evolved Stand, The World Over Heaven.
Chapter 10:
The Joestars reappear at Air Supplena Island. Johnny is angered that his attack could not do a thing to DIO. Giorno states that he could feel as if The World Over Heaven had nullified Gold Experience Requiem's momentum, and had never seen anything like it. At that point, Valentine appears and challenges Jotaro to a fight, as he wants to witness the power of Star Platinum. After the fight, Valentine has figured out that Star Platinum and The World are the same type of Stands, even after the Stands evolving, much like Jotaro's adult self from 11 years in the future, which is why DIO could not take Jotaro's Corpse Part. He explains that his goal had always been gathering the Corpse Parts, but Johnny had captured him with his Infinite Rotation technique, so he used Dirty Deeds Done Dirt Cheap to escape to a parallel Earth which, incidentally, was very similar to the main Earth - except that, in that parallel Earth, DIO was not defeated by Jotaro; instead, the opposite happened, and DIO evolved his Stand to the maximum as he took over the world. Valentine then tried to bring DIO over to destroy Johnny, but his Stand was too overwhelmingly powerful; his ambition far more dangerous than he anticipated. Realizing that the world he ruled was only one of many, DIO decided to invade the main world and conquer it. Valentine then confesses that he wishes to defeat DIO; he pretended to be loyal and help him invade the original universe, while seeking someone who could defeat him, and found that someone in Jotaro. Valentine himself could not figure out any secret behind the power of The World Over Heaven, but he noticed how DIO could not steal the Corpse Part held by Jotaro, and realized that could not have been a coincidence. He says that he does not want the Corpse Parts for the power to invade worlds, but for the prosperity of his country and its citizens, but he alone cannot avoid DIO's conquering march over the United States, as well as the rest of the world. He states that finding the secret to DIO's power is the key to defeat him, and only Jotaro can do that. He then gives DIO's plan away, telling the Joestars to recover the stolen Corpse Parts so they can turn the tables. Valentine also confirms to Joseph that identical objects/beings from different timelines within the same world can safely interact with one another, after Valentine demonstrates the effects between his gun and his counterpart's gun which was stolen by Johnny. Lastly, Valentine points out that while DIO was defeated in the main world, there are still his mortal remains. He explains that when something from a world meets the same thing from another world, they extinguish each other. DIO's case is different, though, since he no longer exists in the main world. Jotaro points out that he left DIO's corpse under the sun to burn away, and was sure nothing was left of him, but Valentine replies that some of DIO's missing remains still lie where he was defeated by Jotaro. After a brief demonstration of his and Johnny's guns colliding and effectively destroying each other, Valentine decides to end the conversation, leaving the Joestars to decide whether to believe him or not, but hoping they will make the right decision. Johnny remains reticent about not trusting Valentine, and Speedwagon wants to figure out an explanation for DIO's powers, but Jonathan reminds them they now have to retrieve the Saint's Corpse Parts. Giorno then asks Johnny whether he felt DIO's counterattack repelling Tusk ACT4, and Johnny says it was more like he nullified his attack. Giorno says that he felt DIO's Stand similar to Gold Experience Requiem, but with an opposite power: in the fight, he sensed that DIO used his power to "overwrite the truth" of their attacks getting through to him. Speedwagon dismisses the notion, stating that this would make it impossible to beat DIO, but Jonathan says he will fight all the same, if only to figure out DIO's weakness. The others also give their reasons to fight, concluding with Jotaro offering four good reasons to fight: to retrieve the Saint's Corpse Parts, bring back the friends DIO has been manipulating, find out the secret to his power so he can be defeated... and because he's getting tired of DIO.
Afterwards, Jotaro heads for Morioh-Prime, as he would likely find a Corpse Part holder there. He soon finds D'Arby back at the Cafe Deux Magots. He goes to propose him a gamble. If D'Arby wins, Jotaro lets him take his soul along with his Corpse Part; if Jotaro wins, D'Arby will have to surrender his Corpse Part and tell him the secret of DIO's Stand. D'Arby gets nervous for a moment, but says that the detailed knowledge of DIO's power is far away from him; however, he agrees to wager a "name". Jotaro manages to defeat him again, and D'Arby, after surrendering his Corpse Part (the left arm), gives Pucci's name as the only one who knows about DIO's power, as his right-hand man. He also reveals that DIO's power has one thing in common with his Stand: they both have a relation with souls. While D'Arby collects souls for fun, DIO needs souls to manifest his power. Jotaro muses whether that has any relation to DIO's notes that he burned after destroying him. D'Arby then suggests that Jotaro look for Pucci, since he has no more information than what he has just said.
The next stop is the village in the Rocky Mountains in the parallel world, where Okuyasu and Stroheim appear before Jotaro. They both challenge him for his Corpse Parts, but the young Joseph and Josuke 4 soon appear to even the odds. With both of them defeated, Jotaro manages to heal them with his Corpse Part, just as Will Zeppeli and Gyro show up to battle. Sure enough, Jonathan and Johnny appear to take matters into their hands. Once defeated, they too are healed, and Jotaro retrieves the Corpse's heart while Jonathan explains the situation to the others, who accept to join the heroes.
Jotaro then travels back to 1988 Cairo, right at the bridge where he defeated DIO. There he finds DIO's bracelets and, remembering what Valentine said about identical objects/beings from different worlds cancelling each other out, believes that they might be useful.
Next, at Napoli Train Station, Jotaro is challenged by Bucciarati, when Giorno, Mista, Trish and Narancia all step up to battle him. Bucciarati is also defeated and healed, and Jotaro retrieves the Saint's Corpse's ears. After Giorno explains to him the situation, Bucciarati agrees to lend his aid.
The next stop in the trip through time is at Green Dolphin Street Prison, where Yukako appears to challenge Jotaro. Koichi is brought out along with his friends. Josuke 4 is worried about Koichi, but the boy assures him that he will fight to save Yukako. They manage to defeat her and bring her back to her senses, when Josuke 4 senses someone else coming: it is the two Kiras, stating that they do not really care for DIO's mission, but are there to get their revenge on Josuke and his friends. They are defeated, but swear that this is not the end and they will come back to kill each and every one of the heroes if they dare disturb their "tranquility" again. After they leave, Jotaro recovers the Corpse's right arm that the Kiras left behind, while Koichi fills Yukako in on what has been happening so far.
At the rebuilt Joestar Mansion, Pucci informs DIO that Jotaro has managed to retrieve half of the Corpse Parts he entrusted to his "pawns", and brought a number of them back to normal. DIO is not worried, because the Saint's Corpse is influenced by its owner, which may cause its spiritual strength to grow bigger, and the Parts are simply means to an end. What is important at the moment are "the souls of more than 36 sinners". He states that the criminals that turned their backs to heaven are influenced by the Joestar bloodline, and may eventually stand against him. This is why he will have to absorb these sinners' souls, to uphold his conviction of conquering the world. Pucci then tells DIO that "he" was found as one of the sinners. DIO says he will deal with him and starts to leave, when Pucci asks him, in case those souls weren't worth sacrificing, if he would do away with him. DIO answers affirmatively and leaves. Left alone, Pucci asks those who would hinder their way to Heaven to protect their souls.
Chapter 11:
The next stop in the quest to retrieve the Saint's Corpse Parts is Boing-Boing Cape in Morioh, where Shigechi and Otoishi instantly appear to challenge Jotaro, Josuke 4 and Okuyasu. After they are defeated and healed, Weather Report appears and is confronted by Jolyne and Anasui. Like the others, he is brought back to his senses once beaten. Jotaro then retrieves the Saint's Corpse's head.
In the meantime, Valentine appears in 1988 Cairo, now very tired after trying to escape through multiple parallel worlds. He is suddenly brought before DIO, who has heard that Valentine told the Joestars about his power, and asks if he is planning a way to defeat him. After a long time of hesitation, Valentine speaks up and says that what he wants is justice, and attacks DIO, who simply uses The World Over Heaven to erase Valentine from existence.
Back to the heroes, they head to the Colosseum next. At first, nothing seems to be happening, but then Giorno and the others sense that time has been subtly accelerated, and they come to one conclusion: they have come within range of King Crimson, Diavolo's Stand. Diavolo shows up, revealing his intention of defeating Giorno first. After he is defeated by Giorno and Trish, Diavolo surrenders his Corpse Part (the legs) to them and leaves.
Returning to Air Supplena Island, the group is confronted by Diego and Dio, who are defeated once again and flee. Before Jotaro can take another step, Avdol and Iggy appear before him to fight, so Joseph, Kakyoin and Polnareff are brought out to bring their friends back to normal. Once Avdol and Iggy are defeated, they too are freed from DIO's control with the power of Jotaro's Saint's Corpse Part. While Joseph decides to tell Avdol the whole story later, Polnareff takes the time to try and get friendly with Iggy, who inevitably attacks him.
Next, Jotaro heads for the Joestar Mansion, where Pucci is waiting. Pucci already knows what Jotaro is going to ask him, and says that there is nothing they can do against DIO's power, going on to say that those foolish enough to oppose him will face Heaven's judgement, as zombies come out to attack. Once they are dealt with, Jotaro asks if Pucci will come and fight, to which the priest says they are in a place of destiny, as it was in the Joestar Mansion where everything began. There, DIO showed him his destiny: a higher path to Heaven to walk on and to guide people through, and he will demonstrate the Heaven he is aiming for to those before him now. That is the "truth", and those who receive it will receive bliss, thus the "Eyes of Heaven" he seeks are a plan for the people's salvation. However, Jotaro doesn't care for this, and seeing it would be a waste of time to pry DIO's secrets from Pucci, he decides to show him his own power instead. Despite being defeated by Jotaro and Jolyne, Pucci knows that the young Jotaro will summon older Joseph to uses Hermit Purple to find the weakness of DIO's new form in which Pucci knows inside his memories, and says that he feels a strange tranquility, because DIO is close to the next step in his goal: the souls of the "36 Sinners" are those of the very expanded Joestar Group; DIO intends to offer them as his sacrifices. He says that, in the world's current state, each person has only one soul, but wonders what if they could have more and what would happen. After proclaiming his love for DIO, Pucci then commits suicide by throwing himself from a balcony and is impaled on the Love Goddess's statue, thus preventing the heroes from finding out DIO's weakness. Even with this setback, Jotaro proceeds to retrieve the Saint's Corpse's eyes.
Chapter 12:
The JoJos and Speedwagon return to Egypt to confront Heaven Ascension DIO in order to stop him. Jotaro and Jolyne face DIO in battle where he demonstrates his power, including the ability to turn Jolyne against Jotaro. Jotaro and Jolyne seemingly defeat him, only for DIO to immediately heal himself and reveal that his real motive was to mark Coco Jumbo with The World Over Heaven, thus obtaining it and thus all of those inside the turtle. Jotaro and Jolyne prepare to battle DIO once again, while the other JoJos and Speedwagon go forth into other worlds to face an ally once again in three different battles. However, Giorno realizes too late that it's all a ploy by DIO to separate the other JoJos from Jotaro and Jolyne, thus allowing him to kill the other JoJos and Speedwagon before absorbing their souls, along with all of their allies' souls and the Saint's Corpse Parts. Further empowered, DIO rewrites the universe to his own liking, but Jotaro and Jolyne stand in his way. After a final showdown, DIO kills Jolyne and absorbs her soul before preparing to destroy Jotaro once and for all. This does not work out properly for DIO, when Star Platinum (which is the same as DIO's) evolves to become Star Platinum Over Heaven, overwriting DIO's reality. The fight proceeds and DIO appears to once again gain the upper hand and attempts to finish Jotaro off. However, having remembered Valentine's warnings about identical objects/beings from different worlds not being able to exist simultaneously, Jotaro pulls out the original DIO's bracelets, which fuse with Heaven Ascension DIO's bracelets and destroy his hands, thus making him unable to use The World Over Heaven. Enraged by this, Heaven Ascension DIO tries to deliver a fatal blow (by repeating the original DIO's final, fatal mistake and attempting to blind Jotaro with his own blood), but Jotaro successfully retaliates and kills DIO with one final punch, once again stating that he only did it because DIO "pissed him off".
As a result of Heaven Ascension DIO's death, all of the timelines and realities are restored and Jotaro returns to meeting Joseph and a fully-healed Polnareff. They're informed that Kakyoin, Avdol and Iggy are resting in Cairo Hospital, as Jotaro realizes that he's in a new timeline, which gives him a sense of deja vu, having prevented their deaths in the previous timeline. After visiting the previously-deceased, Jotaro, Joseph and Polnareff return to the airport, where Jotaro and Joseph head back home, while Polnareff stays behind in Egypt to take care of his friends after the end of another bizarre adventure. After Jotaro and Joseph depart for Japan and promise to return to Egypt to visit their friends after they make a full recovery, the scene ends with Kakyoin, Avdol and Iggy recuperating in Cairo Hospital.
After the credits are shown, a photo montage shows events that happen in the JoJo universe as a result of the new timeline:
- Jonathan facing off against Dio, with a surviving Will Zeppeli at Speedwagon's side looking on.
- Joseph and a surviving Caesar facing off against Wamuu and a surviving Esidisi together at the Skeleton Heel Stone.
- Josuke 4, Koichi and Okuyasu hanging out together with a surviving Shigechi, with the real Kosaku Kawajiri walking by the group.
- Giorno as the new boss of Passione, with all the members of Team Bucciarati (including Leone Abbacchio) at his side.
- Jolyne shown together with Ermes, Emporio, Anasui, Weather Report and a middle-aged Jotaro.
- Johnny and a surviving Gyro battling the alternate Diego Brando.
- Josuke 8 together with Joshu, seemingly getting along.
- Jotaro and Joseph reuniting with Polnareff, Avdol, Kakyoin and Iggy at the airport.
Epilogue: 11 years after the events of the game (after Part 3's new timeline), Koichi encounters an incredibly tall man arriving in Morioh, accompanied by his young daughter. He had decided to bring her along because she kept throwing tantrums. After she runs off to look at a turtle, the tall man asks Koichi about the location of a certain Josuke Higashikata...
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