England, 1868. A notorious cutpurse by the name of Dario Brando comes across the site of a carriage accident. As he pillages the valuables from the affluent passengers, one of them suddenly regains consciousness. This man, George Joestar, mistakenly believes Dario to have saved him and places himself in his debt.
Both men are also fathers. George's son, Jonathan Joestar, grows up with a hot temper, but also a strong sense of morality and strives to be a perfect gentleman. Dario's son, Dio Brando, is cunning and callous. Eventually, Dario falls gravely ill and, on his death bed, instructs Dio to seek out the Joestars, and find some way to take their fortune for his own. Dio has no love for his father, an abusive drunk who had worked his mother to death, but undertakes the task nonetheless, if for no other's sake than his own.
Dio is adopted into the Joestar family as a favor from George to Dario. Immediately, Dio sets out to drive Jonathan to insanity, winning his father's favor and isolating him from his friends. Jonathan finds some solace in his budding friendship with a young girl from the countryside named Erina Pendleton, but Dio throws a wrench into their relationship by stealing Erina's first kiss, making her too ashamed to face Jonathan. After realizing what happened, Jonathan starts a fight with Dio and beats him badly, humiliating him. In retaliation, Dio traps Jonathan's beloved pet dog Danny in an incinerator.
With Danny's death, Jonathan becomes too frightened to confront Dio for the next seven years. In that time, the two appeared to finally bond and become like brothers, but Jonathan's fear of Dio, and Dio's disdain for Jonathan, make their camaraderie a mere show.
Around the time the two young men graduate from university, George Joestar begins to fall ill. While doing research on a stone mask that had been in the Joestar family's possession for many years, Jonathan comes across a letter that Dario wrote to Dio before his death. To his horror, the symptoms that Dario described mirrored George's, leading Jonathan to realize that Dio was poisoning his father! Jonathan confronts Dio about the matter, and Dio attempts to intimidate Jonathan into letting the matter slide. Jonathan, however, musters the courage to press on, and takes advantage of Dio's pride to confirm his suspicions. He leaves George in the care of the most trusted physicians while he takes the "medicine" to find a cure.
Jonathan's research into the poison leads him to Ogre Street, a particularly notorious slum in London. There, he is confronted by Robert E.O. Speedwagon, a mugger and gang leader who attempts to rob Jonathan. Jonathan manages to fight him and his goons off, to Speedwagon's surprise, without injuring them seriously. When Jonathan explains that he came for his family's sake and didn't want to cause any grief to the families of Speedwagon and his underlings, Speedwagon, taken aback by Jonathan's generosity, lends his aid to Jonathan's cause.
Meanwhile, Dio begins to plot Jonathan's murder. The stone mask, according to Jonathan's research notes, creates stony tendrils that burrow into the wearer's skull and brain when it comes into contact with blood. Thus, Dio plans to use the mask to kill Jonathan and make his death appear to be an experiment gone wrong. Even though Jonathan's travels to Ogre Street leaves him certain that his rival would not return alive, Dio decides to test out the mask on a random drunkard. To his horror, the mask doesn't kill his victim, but turns him into a vampire! It is only by the light of a rising sun that Dio is spared from a grisly demise.
Upon returning to the Joestar manor, however, Dio is confronted by Jonathan, Speedwagon, George, and the police. Jonathan had found the apothecary that made the poison for him, and he was to be arrested. In a last ditch effort to evade capture, Dio tries to stab Jonathan so he can use his blood to activate the stone mask on himself. George takes the fatal blow for his son, and Dio uses his blood to activate the mask and transform himself into a vampire, slaughtering the police and chasing Jonathan through the manor. A desperate Jonathan sets fire to the mansion and impales Dio on a statue, leaving him to burn with his childhood home and barely escaping with his life.
While recovering from his fight with Dio, Jonathan is reunited with Erina, who had been tending to his wounds. As the two rekindle their friendship, Jonathan meets a peculiar man named Will A. Zeppeli, who informs him that Dio still lives! However, there is a way to fight back against Dio: the martial art of Hamon, which allows its practitioners to convert their vital energies into sunlight via special breathing techniques, thus letting them combat the undead. Jonathan proves to be a natural at Hamon, and sets off with Zeppeli and Speedwagon for Windknight's Lot, a village where Dio had taken up refuge. Along the way, Jonathan tests his mettle against the infamous Jack the Ripper, whom Dio turned into a zombified minion, and who Jonathan manages to overcome in the first true test of his Hamon prowess.
The group eventually encounter Dio, who sicks two revived knights of the famous Mary, Queen of Scots, on him: Bruford and Tarkus. Bruford, who attacks Jonathan with prehensile hair and a sword, tries to leave Jonathan powerless by fighting him in a lake, leaving him unable to breathe and thus unable to use Hamon. Jonathan, however, manages to find an underwater air pocket and uses it to attack Bruford. While his attack does not hit Bruford directly, the indirect exposure to Hamon restores Bruford's humanity. Before the Hamon disintegrates his body, Bruford bestows upon Jonathan his sword of "Luck", adding a "P" in blood to transform it into a sword of "Pluck".
Tarkus, who is far more menacing and cruel, goes on the attack. Jonathan, Speedwagon, and Zeppeli escape to a nearby castle, where knights used to train. Tarkus places a collar on Jonathan, attached to a chain with another collar around Tarkus's neck, and the zombified knight uses his immense strength to try to strangle Jonathan. Zeppeli, realizing that the events playing out before him were the same as a prophecy he received from his Hamon instructor that foretold his death, sacrifices himself to give Jonathan the chance he needs to defeat Tarkus. With his dying breath, Zeppeli bestows upon Jonathan the last of his Hamon, giving him the strength he will need to defeat Dio.
Along the final stretch to Dio's castle, Jonathan is joined by other Hamon practitioners: Tonpetti, Zeppeli's instructor, and Dire and Straizo, his proteges.
Upon reaching Dio's castle, Dire attempts to attack Dio, but is killed when Dio freezes and shatters his body. Jonathan fights Dio, with Dio gaining an advantage due to being able to freeze Jonathan's sword and hands. Jonathan, however, manages to use a nearby sconce to melt the ice, giving him the opportunity to land a Hamon-infused blow to Dio's body, sending him falling from the castle as his body disintegrates.
With Dio vanquished and the stone mask destroyed, Jonathan marries Erina and leaves on a steamboat with her to celebrate their honeymoon in America. The festivities are interrupted by zombies attacking the boat's passengers. In the boat's engine room, Jonathan finds Dio, having been reduced to a head in a jar carried by a zombified underling. Dio attacks Jonathan, severing the major arteries in his neck with eye beams to weaken his Hamon. Realizing that the two were bound by fate, Dio is determined to take Jonathan's body for his own. Jonathan, in a last ditch effort to defeat Dio once and for all, uses the last of his Hamon to drive Dio's underling to sabotage the boat's engine.
Erina finds the mortally wounded Jonathan and, unable to bear the thought of going on without the love of her life, resolves to stay with him to the bitter end. Jonathan, however, tells Erina to live on and to save a nearby infant whose parents were killed by zombies. As Erina escapes, Dio makes one last effort to kill Jonathan, but Jonathan manages to subdue Dio's head.
Dio desperately tries to bargain with Jonathan, promising him and Erina eternal life.
His pleas, however, fall on deaf ears: at that point, on February 7, 1889, Jonathan Joestar dies.
The steamboat explodes shortly thereafter. Erina survives, having taken the infant with her into a special coffin that Dio made to withstand such explosions. As she is rescued just off the Canary Islands shortly thereafter, she vows to tell the tale of Jonathan Joestar's bizarre adventures to her unborn child...