As an infant, his mother died in a carriage accident. That same accident indirectly brought Dio Brando into his life, because Dario, Dio’s father, unwittingly saved Jonathan’s father while he was preparing to steal from the wrecked carriage. Twelve years later, Dario apparently died of illness and Dio went to live amongst the Joestars. Dio, despite Jonathan trying to be friends with him, would become his nemesis both as a childhood rival and as an undead enemy. At the young age of 12, when Dio came into his life, he meets and falls in love with Erina Pendleton, but Dio shatters this relationship for a considerable time through his evil ways, by kissing Erina and boasting about it.
Nonetheless, Jonathan is able to maintain his sanity and his studies in archaeology. Among his interests is research on a Mesoamerican stone mask that is part of the estate. Curiously, the mask sprouts spikes that pierce the wearer’s skull if human blood touches it. Finally after eight years, Jonathan takes a stand against Dio when he discovers that Dio poisoned his own father with a substance that imitated illness, and his plot to poison George in the same way and take over the family fortune. So JoJo travels to ogre street in order to find an antidote which he finds thanks to the help of his new comrade Robert Edward O Speedwagon. In their fateful encounter, Dio stabs George while wearing the mask–Dio has learned that the mask is not a killing device, but a means to let the wearer transcend humanity and mortality (and anything resembling moral restraint) to become a mighty vampire.
In the first confrontation with this new monster, Jonathan holds his own, but in his desperation to destroy Dio, Jonathan sets fire to the manor. in the battle, Jonathan, torn by the losses caused, grabs Dio and pulls him down many floors, ultimately impaling him on a goddess statue. However, Jonathan suffers horrible burns and is taken to hospital, whereas Dio is able to escape unseen. Robert E.O Speedwagon watches Jonathan being looked after and finds out that the nurse taking care of him is Erina, who had gone to India after Dio disgraced her and Jonathan’s relationship–but not, after all, extinguished it. Shortly after being discharged from the hospital. Jonathan is taken in by Will Zeppeli, who teaches him hamon in order to defeat Dio. He travels with Zeppeli and Speedwagon to the town of Windknights to confront Dio. On his quest he faces many enemies such as Jack the Ripper and Bruford and Tarkus. And once again manages to seemingly defeat the vampire.
Shortly after the Windknights battle, Jonathan and Erina marry, and soon set sail for America for a honeymoon. Their trip is cut short by an attack by Dio, now only a severed head, and Jonathan makes the supreme sacrifice, staying aboard the sinking ship in an attempt to take Dio down with him. Erina, pregnant with Jonathan’s child, escapes the shipwreck.