In the quiet, picturesque Japanese town of Morioh in 1999, strange events begin to surface. High school freshman Josuke Higashikata discovers he is the illegitimate son of Joseph Joestar and the uncle of Jotaro Kujo, a man who arrives in town to investigate a growing number of supernatural incidents. Josuke possesses a powerful manifestation of his life energy called a Stand, named Crazy Diamond, which has the remarkable ability to restore any damaged object or person to their original, undamaged state, though it cannot heal the user himself or revive the dead. Jotaro, wielding the time-stopping Star Platinum, reveals that a mystical Bow and Arrow is being used to create new Stand users across Morioh, and not all of them have peaceful intentions.

As Josuke and his timid but brave friend Koichi Hirose delve deeper, they confront a depraved serial killer named Anjuro Katagiri, known as Angelo, who uses a water-based Stand called Aqua Necklace. After a fierce battle, Josuke defeats Angelo and enacts a unique form of justice by using Crazy Diamond to fuse him permanently into a large rock, leaving the killer as a grotesque part of the town's landscape. The search for the Bow and Arrow leads them to the Nijimura brothers, Keicho and Okuyasu. Keicho has been using the Arrow to randomly pierce citizens, hoping to create a Stand powerful enough to end the suffering of their mutated, immortal father. In a climactic confrontation, Keicho is struck down not by Josuke or Jotaro, but by a hidden enemy named Akira Otoishi, who uses the electric Stand Red Hot Chili Pepper to kill Keicho and steal the Arrow. Moved by his brother's death, the simple-hearted but powerful Okuyasu, whose Stand The Hand can erase anything it swipes, joins Josuke's group to seek revenge.

The narrative shifts from a straightforward hunt for the Arrow to a darker, more suspenseful mystery as the team pursues Otoishi. After a series of battles across Morioh, including a tense showdown at a critical electric power station, they finally defeat the arrogant guitarist and reclaim the Arrow. With that threat neutralized, peace briefly returns to Morioh, allowing Jotaro to take custody of the Arrow. However, the film closes with the ominous introduction of a seemingly ordinary and handsome office worker named Yoshikage Kira, a serial killer who has been operating undetected in the town for years. Driven by a fetish for women's hands and a desperate need to live a quiet, peaceful life, Kira possesses the devastating Stand Killer Queen, capable of turning anything it touches into a bomb. His presence sets the stage for an uncaught threat far more terrifying than any Stand user they have faced before.