Josuke and Okuyasu come across a peculiar person named Mikitaka Hazekura who claims to be an alien. Believing his claims to be a joke, Josuke initially suspects him to be a Stand user when he exhibits some strange abilities. However, upon being distressed by the sound of sirens, Mikitaka suddenly transforms his body into a pair of sneakers and flees with Josuke, who realizes he is not a Stand user as he cannot see Crazy Diamond. Looking to take advantage of Mikitaka's transformation ability, Josuke has Mikitaka transform into some dice and challenges Rohan to a game of Cee-loW in the hopes of winning some money off of him. As the match begins, Josuke grows worried when Mikitaka seems to get suspiciously ideal rolls.
Becoming suspicious of Josuke's winning streak, Rohan stabs his own finger, staking two million yen against Josuke's own finger to determine how he is cheating while also calling upon Tamami Kobayashi as an official to prevent Josuke from playing normally. Just as Mikitaka becomes unnerved by sirens and starts to lose his transformation, Rohan is distracted upon discovering he had accidentally set his house on fire, allowing Josuke to escape without being discovered. The next day, while riding a bus through a tunnel with Josuke, Rohan spots a window to a room revealing a man cutting off a woman's hand, believing it to be Kira. Returning to inspect the tunnel, Rohan discovers the room to be an illusional trap, suddenly finding himself attacked by a nutrient-sucking Stand named Highway Star. When Josuke comes to the tunnel, Highway Star tries to use Rohan to lure him into his room. As Josuke ignores Rohan's warnings and enters the room anyway, Rohan sends him flying out of the tunnel, urging him to flee from Highway Star and find his user.
Believing there is connection between Highway Star's user and the Futatsumori Tunnel he resided in, Josuke gets in contact with Koichi, who suspects the user to be someone hospitalized from a traffic accident stealing nutrients to heal himself. While Josuke makes his way to the hospital while keeping ahead of Highway Star, Koichi manages to find out the identity of its user, Yuya Fungami. Despite being caught by Highway Star upon reaching Yuya's room, Josuke manages to recover his nutrients with an IV drip, healing Yuya's injuries so he can pummel him without guilt. Meanwhile, at the Kawajiri household, Shinobu finds a British Blue cat hanging around the basement.
Upon discovering the cat to have a hole in its throat, Shinobu sends Kira down to the basement, where he discovers the cat had been killed by glass shards during its struggle with Shinobu. After being buried in the garden, the cat mysteriously comes back to life in the form of a strange plant known as Stray Cat, possessing the ability to control air. Discovering Stray Cat to be the cat from earlier and realizing it has a strong grudge against Shinobu, Kira ends up shielding her from its attacks, eventually stopping it by appealing to its cat-like nature. The next day, Hayato discovers Stray Cat while investigating the attic, coming under attack after he exposes him to sunlight. Managing to use Stray Cat's air attacks to put it back to sleep, Hayato barely manages to avoid being discovered by Kira, who he realizes isn't his real father.
Yoshihiro, recognizing Kira in his new appearance, notices he is being followed by Hayato. Later, on July 15th, Josuke and Okuyasu come across Mikitaka, who spots a Stand user named Toyohiro Kanedaichi living on an electrical pylon. When Josuke spots Yoshihiro with him, he steps inside the pylon and falls under the spell of Toyohiro's Stand, Super Fly, becoming trapped inside until someone else takes his place. Josuke and Okuyasu attempt to destroy the pylon, only to discover it dishes out any damage it takes. Wanting to help, Mikitaka confronts Toyohiro, helping Josuke escape but becoming trapped himself. Meanwhile, as something troubling happens in the Higashikata household, Rohan, who had noticed Hayato's behavior, is approached by a strange man.
Rohan is greeted by Masazo Kinoto, an architect sent to evaluate the damages done to his house, using his Heaven's Door to find nothing suspicious besides an aversion to people looking at his back. Meanwhile, Josuke climbs up the pylon to rescue Mikitaka and confront Kanedaichi, who uses calculative cuts on the pylon to attack Josuke from all angles. However, Josuke manages to use Crazy Diamond's healing ability to send the bolts of energy back to their origin and defeat Kanedaichi. Resigning himself to stay inside the pylon, Kanedachi reveals that he heard Yoshihiro say that another Stand user has allegedly eliminated Koichi. Enlisting Yuya's help in tracking Koichi's scent in exchange for healing his injuries, Josuke encounters the Stand user, Terunosuke Miyamoto, who unbeknownst to him had used his Stand Enigma to turn Koichi and Tomoko into pieces of paper after witnessing their ticks when they are afraid.
Overcome by his curiosity, Rohan lays a trap for Kinoto so he can see his back. The moment he does, however, a Stand possessing its own will named Cheap Trick bursts from Kinoto's back and attaches himself to Rohan's back instead, demanding that he burn the pictures he had taken of Kira suspects. Meanwhile, Miyamoto reveals that he has trapped Koichi in a piece of paper, managing to prompt Josuke into biting his lip and falling under Enigma's power himself, becoming trapped as well as a result. Despite not wanting to get involved, Yuya becomes moved by Josuke's resolve and goes after Miyamoto, encountering several paper-hidden traps that eventually culminates in a shredder that threatens to shred both Josuke and Koichi. Despite being overcome by fear and falling under Enigma's power, Yuya manages to take advantage of his now paper-like state to reach into the shredder and free Josuke and Koichi, who quickly deliver their vengeance on Miyamoto who winds up in the form of a book.
Unable to get Koichi to take him seriously without exposing his back and passing Cheap Trick onto him, Rohan attempts to make his way to Morioh Grand Hotel without letting anyone see his back. Cheap Trick attempts to attract several cats and dogs to attack Rohan and witness his back, but they are shooed off by Koichi, who eventually comes to believe Rohan's story. Koichi attempts to forcibly remove Cheap Trick using Echoes ACT3, only to discover that doing so will damage Rohan as well. Despite this, Rohan succeeds in his ultimate goal to lure Cheap Trick into Reimi's Ghost Alley and trick him into turning around, getting dragged into HellW by the alley's hands as a result. Meanwhile, Hayato witnesses Kira killing a couple with his ability and catches it on film, something that Kira is quick to notice. Kira confronts Hayato and prepares to kill him, only for Hayato to reveal he has set up further cameras and videotapes that would threaten to expose his identity.
Kira inadvertently kills Hayato before learning from Yoshihiro that Rohan and the others now have Kosaku Kawajiri as one of their suspects. As Kira becomes anxious over what he should do, he is suddenly impaled by Yoshihiro's Arrow, giving Killer Queen a new ability. The next morning, Hayato appears alive and well, as if nothing had happened to him the previous night, noticing Kira has a strange confidence about his position. Later that morning, Hayato comes across Rohan, who uses Heaven's Door to read his memories. After reading several pages predicting occurrences moments before they happen, Rohan comes across a page revealing Kira's identity. It is at this moment, however, that Kira activates the third bomb that he had implanted in Hayato, Bites the Dust, which is set to kill anyone who learns about Kira's identity through Hayato. As the explosion goes off inside of Rohan's body, Hayato suddenly finds himself sent back in time to an hour earlier due to Bites the Dust's effects.
Hayato tries to avoid meeting Rohan, only to discover the events that occurred last time will still happen even without him being there, resulting in Rohan's death by Bites the Dust's explosion. When Josuke's group arrive at the scene shortly afterwards, Hayato attempts to kill himself to avoid being found out. However, he is stopped by Killer Queen, who sets off Bites the Dust in Josuke and the others and once again returns Hayato to the start of the morning. Realizing that he can only stop Kira by either killing him or forcing him to undo Bites the Dust, Hayato hides Stray Cat in his backpack, launching a surprise attack on Kira when he follows him later in the morning. However, because of a slight alteration of events due to Hayato's actions, Kira manages to protect himself from Stray Cat's attack with a watch he had put in his jacket.
As Kira brags about his victory to Hayato, he unknowingly reveals his own identity to Josuke, who Hayato had secretly called ahead of time. Needing Killer Queen to protect himself, Kira is forced to undo Bites the Dust, preventing Rohan from being killed by its effects. Engaging in battle against Josuke and Okuyasu, Kira manages to retrieve Stray Cat and use its air shots to create invisible remote bombs, dealing heavy damage to Okuyasu. As Josuke tries to reach Okuyasu in order to heal him, Hayato deduces that Okuyasu's body might have been turned into a bomb, leaving Josuke with the tough decision of whether to sacrifice himself to save Okuyasu. However, Hayato, deducing that Kira can only set off one bomb at a time, sets off the bomb on himself, allowing Josuke to heal both him and Okuyasu. As Kira launches another air bomb, Josuke, refusing to believe Okuyasu might already be dead, manages to use Crazy Diamond on debris in his wounds to dodge the explosion.
Despite Josuke and Hayato hiding inside the house, Kira manages to figure out Josuke's location and send an air bomb after him. Although Josuke gets hurt in the explosion, he manages to use his hardened blood on a vase fragment, turning it into a homing bullet that manages to hit Kira. Noticing Kira carrying a cell phone with him, Josuke deduces that Yoshihiro had been hiding in Hayato's pocket, informing his son of their location, and tricks Kira into killing him instead. Josuke then draws Kira into a close quarters fight, but Stray Cat manages to protect Kira from Crazy Diamond's attacks. Just as Josuke is about to be hit by another air bomb, he is saved by a very much alive Okuyasu, who retrieves Stray Cat from Kira, driving him further into a corner as Jotaro and the others arrive on the scene.
Surrounded by ambulances and fire engines, Kira attempts to use an approaching nurse to activate Bites the Dust again. While initially believing himself to have succeeded, Kira finds himself in Ghost Alley. There, Reimi reveals to Kira that he had in fact died after he was stopped by Koichi and Jotaro and run over by an ambulance. Thanks to the combined efforts of Reimi and Arnold, Kira is forced to turn around and is dragged into the underworld by the alley's hands. No longer bound to her attachments, Reimi and Arnold bid farewell to everyone before moving on to the next life. The next day, Jotaro and Josuke return home as the summer of 1999 draws to a close for the residents of Morioh Town.
In 2001: 2 years after the battle against Yoshikage Kira, Koichi Hirose travels to Italy by Jotaro's favor. He departs Naples Airport to find a boy by the name of Haruno Shiobana. Koichi comes across a peculiar young man who tricks him and drives off with his luggage. Koichi overhears two airport security guards reveal the young man's name as Giorno Giovanna, and infers that Giorno might be Haruno Shiobana. Meanwhile, Giorno meets with the gangster Leaky-Eye Luca, who attacks Giorno and is put into a coma after his attack is reflected back. Giorno reveals his Stand, Gold Experience, and creates a tree to escape from Koichi who caught up to him. Koichi calls Jotaro by telephone, revealing Giorno is the son of DIO. Escaping by train, Giorno encounters Bruno Bucciarati who questions him about Luca's death. Giorno lies to him and Bucciarati goes away. After, Giorno opens his hand only to find an eye enclosed, and Bucciarati reappears behind him and confirms he's lying by licking his face.