Josuke is the fusion between Yoshikage Kira and Josefumi Kujo. Kira was a marine surgeon whose mother Holy fell ill from the Rock Disease, a curse plaguing the existence of the Kira and the Higashikata bloodline. Kira learned of the existence of the Rokakaka Smuggling Organization by accident, and the existence of the Rokakaka, a miraculous fruit which could heal any ailment at the cost of another body part.
Determined to steal the fruit, Kira enlisted the help of Josefumi, a former patient of Holy's who was grateful to Holy for saving his life, and a Stand user. However, Josefumi advised to only steal a branch or two to graft them and get as many fruits as they wanted. Together the two stole branches from under Aisho Dainenjiyama's nose.
Several months later, after the earthquake, the fruits were almost ripe. Kira and Josefumi were confronted by Tamaki Damo and his organization, who managed to learn about the theft and tracked them down. Damo fatally wounded Kira by cutting out his liver, but the latter used Killer Queen to make an explosive distraction, fatally receiving shrapnel in the head. Josefumi and Kira drifted to the place where they kept the only two Rokakaka available, and Josefumi, after fighting off the A. Phex Brothers, used all the fruits to save Kira. An aftershock happened, causing Josefumi and Kira to fall into a fissure. The properties of the ground mixed the two together, and thus Josuke was born.
The protagonist was found buried underground and naked by Yasuho near the Wall Eyes in Morioh.
He shows symptoms of amnesia, as he is unable to identify himself or his residence.
Following the brand of his hat, he and Yasuho visit the shop that the hat was purchased from and from there, they were able to find the name Yoshikage Kira and his address.
When they enter the apartment they found a nice and tidy place.
However, they also found a nude woman in the bathroom whom Yasuho assumed was Kira's girlfriend. The girl did not answer at first, glaring at them before Yasuho found a photo album with pictures of tied up women. Assuming that this was the Josuke's doing, she becomes disgusted and leaves him.
Josuke and Yasuho return to the site of his discovery, finding Kira, who had died three days prior.
Next, Josuke is taken to live with the Higashikata Family, under the name Josuke Higashikata, apparently as a new member. He is given Joshu's room, to his dismay.
Josuke is told by Norisuke to take care of Daiya Higashikata, who suffers from near blindness. After helping her make tea, she tells him to "act natural" before having a piece of her leg destroyed, much to his confusion.He finds himself in the midst of Daiya's California King Bed Stand, before feigning being seduced by Daiya, and finally getting her to step on his shadow in order to retrieve the new memories won by her.
Yasuho receives a DNA result that reveals that the protagonist's and Kira's bodies are a 95.8% match, which seems to conclude that they are the same person.
From the Tree, looking her up, the protagonist learns that Kira's mother, Holy is still alive and currently working at a hospital.On the way, he is attacked by Kyo Nijimura and her Stand Born This Way; while he is assisted by the Stand Paisley Park.
Josuke at first asks Kyo if she attacked him under the orders of the Higashikata's, but Kyo reacts distastefully at the mention of the Higashikata's and insists on killing Josuke if he approaches Holy.
Josuke, at first, is prepared to fight back Kyo, but recognizes her intent and resolves to find another way to approach Holy if it will cause her pain.
As Josuke is about to leave, Kyo asks him to show his tongue and notes that Josuke has two tongues and four eyes.Kyo guides Josuke to the Wall Eyes to somewhat explain his ailment. What she does is hold two fruits together, a lemon and an orange, and buries them. Upon unearthing them, the two each have components of the other switched, with the orange having traces of lemon within and vice-versa.
This puzzles and infuriates Josuke, who cries out questioningly upon who he is and how he came to be, bringing Kyo to tears as well. She explains that Josuke was the result of her brother Yoshikage being fused with someone else, collaterally pointing out that both Josuke and his Stand are similar to Kira and his Stand.
She tells him to investigate the Higashikatas as they may have the answers that he desperately needs.
With Joshu, Josuke combats the community of Shakedown Road; including a mature man who manages a pet shop.
After his victory, he discovers the Joestar Jizo, which the pet shop owner agrees shares its hat with him; sharing that it was donated by the SBR hat shop salesman.
Josuke learns from the pet shop owner of Johnny Joestar, in whose memory the Jizo was erected.
Josuke borrows Joshu's cell phone, calling Yasuho; which she doesn't answer, noticing it as Joshu's call.
Yasuho travels into town in search of Josuke, but he is also affected by the Stand and fails to find her.
The next day, Josuke follows Tsurugi to his underground playroom.
Trailed by Norisuke, Josuke questions him; asking whether he killed Yoshikage Kira, which he says he did not, and in three parts: First, that he knows of the power of the Wall Eyes to combine two objects, and argues that if he wished Kira dead, he should wish the same of Josuke. Second, that he is sympathetic to Kira's family, including Holy, being that theirs shares its fate with his, with respect to the curse of their disease; and third, that he actually needed Kira, believing that he had a clue as to their cure.
Norisuke says that he adopted Josuke in the hope that he has retained these memories; reaffirms his wish for his family's happiness, and that he does not know the identity of the other person composing Josuke, suggesting that he consider himself the individual currently searching for his identity.
Josuke and Norisuke are then targeted by Yotsuyu Yagiyama.
A fight ensues between Josuke, Norisuke and Yotsuyu. Unable to counter Yotsuyu's power, Josuke is initially overwhelmed by the many flower pots attracted to him. However, with Norisuke's help, Josuke manages to get out of I Am a Rock's range a first time. When Yotsuyu touches him again, hundreds of chestnuts are attracted to him, but he and Norisuke manage to hide inside the family bunker.
Realising that Yasuho has been kidnapped by Yotsuyu, Josuke resolves to get out of the bunker and fight Yotsuyu. In the process, he discovers that Yotsuyu isn't a normal human. The fight culminates in Josuke making Yotsuyu sink into the sea, and having Yotsuyu reveal that his original self is connected to Kira before dying. At the same time, Josuke spots the mysterious fruit Tsurugi has been talking about.
Josuke and Norisuke then examine the remains of Yotsuyu and manage to find a fruit. Josuke then follows Norisuke to the latter's fruit parlor in order to identify the fruit, but their search is interrupted when Jobin Higashikata returns.
Because King Nothing smelled the fruit's scent on Jobin, Josuke wants to extract information from him.
To do so, he enlists the help of Tsurugi and challenges Jobin to a beetle fight with the Dorcus Titanus Palawanicus Jobin gave him earlier. He cheats, wins Jobin's Lamborghini, and manages to take the key to Tsurugi and Yasuho so that they investigate Jobin's whereabouts. However, Jobin begins to suspect Josuke and he has to flee.
Josuke meets Yasuho and Tsurugi again the next day. He spends some time with Yasuho, but an unknown woman catches his attention, as she seems to know him.
The woman named Karera Sakunami, is one of Josuke's original self's acquaintance, and Josuke decides to stick with her until she reveals him his name. Karera eventually tells him: his original self was Josefumi Kujo.
Josuke and Karera are then attacked by the A. Phex Brothers, but defeat them both. Karera realizes that Josuke underwent the equivalent exchange, and departs leaving Josuke with still many questions.
Josuke, having heard of the Rokakaka thanks to Karera, starts to research the fruit with Yasuho and Tsurugi, thinking that it may be tied to his identity. His research is interrupted when he witnesses along with the Higashikata Family, Hato bringing her new boyfriend: Tamaki Damo. Thinking that the seemingly awkward boyfriend is nothing suspicious, he quietly asks Norisuke permission to leave, but when he enters the isolated foyer, he notices that Kyo has disappeared and that the house is covered in handprints making anyone who touches them soft. Trying to escape, Josuke accidentally touches the handprints and is softened himself.
Josuke continues to try to find a way to stop the murderous assault caused by Damo in the present while Josefumi and Kira's pasts are revealed in flashbacks.
Josefumi and Kira, having stolen a Rokakaka Branch to use for grafting, are confronted by Damo and the other Rock Humans on Kira's yacht. Damo tortures Kira until the latter manages to escape along with Josefumi using Killer Queen's Sheer Heart Attack. Despite escaping, however, both men succumb to their injuries and die before the Wall Eyes fuse them together during the 2011 earthquake.
In the present, Josuke is surprised to see Hato using her Stand to mercilessly beat Damo to the point of death. After pursuing the fleeing Damo, Josuke confronts the man and avenges the people he's killed by shattering Damo's skull using Soft & Wet. Having come to terms with his different pasts, Josuke confirms his "true identity" as that of Josefumi Kujo.
Josuke can investigate his former identity in peace and confirms that he is an amalgamation of Josefumi Kujo and Yoshikage Kira. Having searched Damo's cleaning shop, his search about the properties of the Rokakaka is also complete.
Josuke then visits the hospital where his mother Holy is treated. Appalled at her condition, Josuke learns that her illness is incurable and the most the doctors could do is put her into an artificial coma to slow the Rock Disease. Feeling a deep attachment to her, and committed to finish what his former selves started, Josuke vows to find the Rokakaka and pay for Holy's treatment.
Having decided to go look for the Rokakaka, Josuke secretly asks Norisuke for help and points out that Jobin is likely to be the Rokakaka Smuggling Organization's ally. Although Norisuke refuses to hear about Jobin, he points Josuke to a plant appraiser who can help him find the branches Josefumi grafted. Josuke then departs to find this man.
Unbeknownst to him, Kaato has been observing them and informs Jobin of Josuke's intention. Jobin thus contacts the Rock Human named Dolomite to help him stop Josuke before he can find his contact. In the streets, Josuke is accosted by a young boy who gives him a letter which, without Josuke's knowledge, contains Dolomite's tooth. Immediately after, Josuke comes under attack from the Stand power named Blue Hawaii. The ability takes control of people or animals making them become feral and relentlessly chase a target, in this case Josuke; moreover, the control transfers from one organism to another through mere physical contact either directly or through infected blood, thus Josuke has difficulty defending himself and opts to flee.
Josuke repels one infectee after the other, but after realizing that he cannot remain on the defensive for long, he calls Yasuho so that she can investigate the tooth he left earlier. While Yasuho conducts her research, Josuke continues to flee from the unending attack of Blue Hawaii. After a while, Josuke is cornered by a baby, and unwilling to harm him, lets himself be controlled by Stand. Josuke then walks up to Dolomite's pond to be interrogated and killed.
Fortunately, Yasuho intervenes and saves Josuke, but not before he reveals confidential information to Dolomite. The cornered Dolomite then reveals that Jobin was the one who asked him to attack Josuke. Moreover, the Rock Human continues to monologue about the worth of the new variety of Rokakaka Josuke is born from.
Josuke and Yasuho take the bus to Mount Hananero, where they seek to meet the mysterious plant appraiser. However, Josuke understands that Dolomite's ramblings weren't random, but a way to warn someone else they weren't aware of but had been listening to them. At the same moment, Josuke sees someone hijacking his bus: it is the plant appraiser he wanted to see.
The plant appraiser announces that they are under attack, prompting Josuke to let him drive the bus, as well as introduce Yasuho. Arriving at a parking lot, Josuke is shown several trees moving slowly through the concrete, proving that a new enemy is stalking them. The plant appraiser then formally presents himself as Rai Mamezuku. Josuke subsequently shows him several photos of the Higashikata orchard he has taken; although Rai discerns the Rokakaka branch, he doesn't reveal anything and prefers to remind Josuke of the stakes of their mission, especially the importance of his safety.
Rai then invites Josuke and Yasuho to take a chairlift, soon revealed to be Rai's summer home. Away from the ground and thus temporarily safe, Rai cooks a creme romanoff for Josuke and Yasuho, who savor the snack. Josuke then listens to Rai's theories about the new enemy, and realizes that the enemy may be a new group. The discussion is interrupted when a tree sneaks near the chairlift. When it whips its branches at Yasuho, she ducks and nearly falls, but Josuke grabs her arm. They see a strange swarm of Stands covering the branches, which attacks Rai's hand, but Josuke neglects him to sweep them from Yasuho's legs. He sends bubbles towards the tree and makes them explode, shattering it. Rai then moves the chair forward to get away from the tree, but being upset, he cuts off his hand and then tosses Yasuho down to the ground, to Josuke's astonishment. Initially angry and threatening to also throw Rai down, Josuke regains his composure and tells Yasuho to go to safe ground.
The enemy appears, and Josuke sends his bubbles to make a makeshift ladder for Yasuho, but several thrown rocks pop them up. Rai manages to stab the enemy while Yasuho uses her Paisley Park to wash away the enemy Stand on her face. Josuke then discovers when the enemy resurfaces that they are two people chasing after them: Urban Guerrilla and his pet Doremifasolati Do.
Urban threatens Rai who has stabbed him but is only knifed a second time. The enemy then plunges undeground, announcing that they have a "killing order". Worried about Yasuho, Josuke jumps down to the ground despite Rai's insistence that he be protected first. Chased by Doremifasolati Do, Josuke sees that his bubbles are ineffective as they get transported behind his opponent. Thus, he is forced to seek shelter at the top of a boulder.
In the meantime, Rai has fallen from his chairlift because of Urban. However, Josuke discerns the determined look on the plant appraiser's face and guesses that he has a plan. He jumps down and runs toward the chairlift's eighth pole, which Rai wanted to reach in order to use the fuel stored in there. Although Josuke is overpowered by the teamwork of Urban and his pet, and ends up crushed beneath Doremifasolati Do, he and Rai manage to gravitate fuel into the Rock Animal and light it up. Doremifasolati Do explodes and Urban is burned alive.
Now safe, Josuke and Rai prepare themselves to go harvest the Rokakaka. Josuke doesn't notice Yasuho leave, but Rai informs him that she had matters to tend to at home.
Josuke and Rai infiltrate the Higashikata orchard through several tunnels. Using a secret passage, they manage to approach the Rokakaka branch, and Josuke observes Rai planting some larvae moths inside the branch and is told to wait two days before a new fruit will grow.
However, when they return through the tunnels, Josuke and Rai begin to feel the effects of an unknown enemy Stand. They decide to go to the surface. Seeing the orchard on fire, Josuke and Rai must now save the branch. Josuke uses Soft & Wet's power to create two great bubbles acting as protective fields against the decreasing pressure. Rai steps outside to take the branch, but the appraiser suddenly meets Poor Tom, the Rock Human responsible for the attack.
Rai tries to attack Poor Tom, strangling him with wires. However, touching Poor Tom results in a dramatic increase in the pressure inside the bubble. Rai is crushed inside the bubble. Josuke then intervenes, putting several poisonous yew seeds inside bubbles and launching them at Tom's mouth, who swallows one of them. Tom then finishes Rai off, takes the branch and tries to flee, hearing the sirens of a fire truck and ambulance and guessing that his allies are coming. Josuke still pursues Tom despite the pressure increasing inside his bubble, and launches another bubble. This multi-layered bubble pursues Tom and manages to corner him just as the ambulances arrive.
Josuke continues to pursue Poor Tom with the bubble until it pops and reveals that there was nothing inside all along. Poor Tom starts running to the ambulance after grabbing what he thinks to be the Rokakaka branch when he is suddenly shot by an unknown assailant, killing him. Josuke sees the person in the ambulance Poor Tom was running towards take the branch and drive away. Josuke despairs over the loss of the branch, but realises that not all hope is lost as Rai is revealed to have survived Poor Tom's attack.