Early YearsAs an infant, his mother died in a carriage accident. That same accident indirectly brought Dio Brando into his life, because Dio's father unwittingly saved Jonathan's father while preparing to steal from the wrecked carriage. Twelve years later, Dario apparently died of illness and Dio went to the Joestars. Despite Jonathan trying to be friends with Dio, the latter 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, Jonathan met and fell in love with Erina Pendleton, but Dio shattered the relationship for a considerable time through his evil ways, by kissing Erina and boasting about it. Learning of this Jonathan came home to confront Dio. Jonathan beats Dio in a fistfight, but a humiliated Dio decides to take revenge by killing Danny, Jonathan's only remaining companion.
Stone MaskNonetheless, Jonathan is able to maintain his sanity and continues 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 intends to poison George in the same way to take over the family fortune. Jonathan then travels to Ogre Street in order to find an antidote, which he locates thanks to the help of his new comrade Robert E. O. Speedwagon. In a fateful encounter, Dio stabs George while wearing the mask (having learned that the mask was not a killing device, but a means to let the wearer transcend humanity, mortality and anything resembling moral restraint to become a mighty vampire).
Battle with Dio
In the first confrontation with this new monster, Jonathan plans to counter Dio's regenerating abilities by setting fire to the manor. After a long struggle Jonathan and Dio plummet into the inferno he created. Dio taunts Jonathan by telling him that his efforts were pointless as he would be able to escape the fire. Jonathan traps Dio inside the burning mansion by impaling him on a statue of the goddess Venus. As Dio curses him Jonathan is blasted outside the manor by an explosion, leaving him with many injuries but still alive.
Jonathan suffers horrible burns and is taken to hospital, whereas Dio is able to escape unseen. Speedwagon finds out that the nurse taking care of Jonathan is actually Erina, who had gone to India after Dio disgraced her and ruined her relationship with Jonathan. However, Dio had apparently not extinguished her feelings for Jonathan. Shortly after being discharged from the hospital, Jonathan meets William Anthonio Zeppeli, who informs him of Dio's survival and begins to teach him Ripple in order to defeat Dio. Speedwagon interrupts their training to inform them of the strange cases of villagers disappearing from Windknight's Lot. On their way there they are attacked by Jack the Ripper, who has been turned into one of Dio's henchmen. Zeppeli decides to have this serve as Jonathan's final test. Zeppeli gives Jonathan a glass of wine and orders him to defeat Jack without spilling a drop of the wine inside. Jonathan realizes that he can detect Jack using the ripples he sees in the wine and defeats him through the wall using a powerful Ripple-charged punch.
The Dark Knights
A boy named Poco makes off with the groups luggage so they give chase, with Jonathan using his Ripple to catch up easier. However, they realize that Poco was being controlled by Dio to lure them to where he and a large number of his minions are waiting. Zeppeli attacks Dio but Dio utilizes his ability to freeze human flesh to debilitate him. Jonathan joins in the fight to parry Dio's attack and prevent him from shattering Zeppeli's arm. Due to Dio's freezing ability the two are not able to damage him with their Ripple.
Dio leaves fighting Jonathan to his henchmen, Bruford and Tarkus. Bruford goes at Jonathan first, wasting no time in using his ability to control his hair and drain blood. Bruford comes at him wielding his sword with his hair but Jonathan is able to narrowly dodge him, falling into the water nearby. Taking their battle underwater Jonathan is at a disadvantage as he is unable to breathe and thus unable to use Ripple. Fortunately he finds air bubbles trapped underneath rocks which he uses to breathe. Using the fact that water carries ripples easily he attacks Bruford. Bruford is able to avoid taking damage but is knocked out of the water. He once again tries to attack Jonathan with his hair but Jonathan channels Ripple through his sword, disintegrating his arm. Jonathan unleashes the 'Sunlight Yellow Overdrive' on Bruford, overwhelming him with a barrage of Ripple-charged punches. As Bruford breaks down he regains his human soul and in respect for Jonathan leaves him his sword.
Tarkus then begins his attack but the group manages to escape when Jonathan and Zeppeli use their Ripple on leaves to create a hang-glider. Tarkus gives chase and forces Jonathan into a Chain Neck Deathmatch at a training ground for knights, with the rest of the group locked outside, unable to help. Jonathan struggles against Tarkus, who is experienced and uses the room to his advantage. With Poco's help Zeppeli is able to enter the room and assist Jonathan against Tarkus, but is bisected and breaks Jonathan's neck in the process. Zeppeli transfers the last of his Ripple energy to revive Jonathan, giving him the strength necessary to defeat Tarkus.
Final Battle with Dio
After Jonathan's fierce battle with The Dark Knights he meets Tonpetty, Straizo, and Dire. Together they set out for Dio's mansion for the final battle. After saving Poco's sister by defeating Doobie he and the rest of the group confront Dio. After Dire is killed by Dio's freezing powers Jonathan gets the idea to counter Dio's freezing by channeling his Ripple through Bruford's sword. Dio summons an army of zombies to take care of the group while he duels Jonathan one-on-one. Jonathan lands a couple of sword attacks on Dio but he survives them with his inhuman powers. Jonathan is able to land a Sunlight Yellow Overdrive on Dio but he quickly puts himself together. Dio grabs hold of Jonathan's carotid artery but Jonathan is able to escape and the two clash one last time. Jonathan's two-handed overdrive wins out and sends Dio plummeting off the edge of the balcony. Believing him to be dead Jonathan's group destroys the stone mask, believing the threat of Dio to be over.
MarriageShortly after the Windknights battle, Jonathan and Erina marry and soon set sail for America on a honeymoon. Their trip is cut short by an attack courtesy of Dio (now only a severed head) who developed a respect for Jonathan and desires his body. Jonathan makes the ultimate sacrifice, using a Ripple to control Wang Chan and destroy the ship while staying aboard in an attempt to take Dio down with him. While the ship is sinking Dio attempts to negotiate with him but his words fall on deaf ears, as Jonathan had already died from his wounds. Erina, pregnant with Jonathan's child, escapes the shipwreck in Dio's coffin along with a baby whose mother was killed by Dio's zombies.
One hundred years later, a coffin is dragged up from the ocean depths - and once open the crew are killed by DIO, who survived the explosion and managed to remove Jonathan's head and merged his own with the rest of Jonathan's body, though the merge is incomplete until he absorbs Joseph Joestar's blood in his fight with Jotaro Kujo. Over the course of four years, using Jonathan's body, DIO impregnates an unnamed Japanese woman with a child that would become Giorno Giovanna, as well as other women with children who would become Donatello Versus, Ungalo, and Rikiel. He also pierces Jonathan's body with the Bow and Arrow, awakening Stands in himself, Jonathan's body and Jonathan's descendants as well.
After DIO's death at the hands of Jotaro he and Joseph expose the body to the sun where its crumbles away, finally ending DIO's feud with the Joestars as well as letting Jonathan finally rest in peace, however years after DIO's death Enrico Pucci, the only person DIO befriended in his whole life finally puts DIO's plan to 'ascend to Heaven' into motion and uses a bone given to him from Jonathan's body to create The Green Baby and later on fuse it with his Stand to evolve it into C-Moon, and again further evolve it into Made in Heaven as he then starts altering the universe, however he was later killed by a barrage of punches from the Stand Weather Report being used by Emporio Alniño. This stopped the universe from further altering and finally put an end to Dio's legacy for good.
Jonathan's counterpart in Steel Ball Run is Johnny Joestar, formally named "Jonathan". Johnny's family also bears noble lineage, but makes its residence in America instead. However Johnny's appearance and personality are very different from Jonathan's.