|“||Give him a bloody nose, and he'll come back twice as fierce!||”|
—Dio assessing Jonathan's determination
As an infant, Jonathan was involved in a carriage accident, resulting in the death of his mother, Mary Joestar. That same accident indirectly brought Dio Brando into his life as his father, George Joestar I, assumed Dio's thieving father saved his life and vowed to repay that debt. Twelve years later, Jonathan comes to the aid of young girl named Erina Pendleton, despite lacking the strength to defend her honor properly. He reveals his intentions of becoming a bonafide gentlemen having opted to help her only to pursue that goal. After meeting Dio, Jonathan's life spirals into hell as Dio attempts to break Jonathan's spirit through dominance and isolation.
At that time, Jonathan crosses paths with Erina; the two become close and eventfully fall in love. Dio learns of this and decides to deny Jonathan any chance of romance by forcibly taking Erina's first kiss, instilling deep shame in the girl. After learning of Dio's deed, Jonathan confronts him at the Joestar Mansion where his resolve for Erina's honor and his dignity gives him the strength to overpower Dio. Jonathan briefly notices the Stone Mask reacting to Dio's blood, but is distracted by his father who attempts to stop the fight before it escalated any further. Despite standing up to Dio, Jonathan was unable to find Erina afterwards, while learning that his beloved dog, Danny, had died after being "accidentally" placed in the incinerator. Jonathan expected Danny's death to be Dio's doing, but Dio had noted the kind of person Jonathan was and decided to feign peace between them for the time being.
Phantom Blood (1888-89)
Seven years later, Jonathan attends Hugh Hudson Academy where he intends to graduate as an archaeologist. During that seven-year span, Jonathan was still wary towards Dio despite his façade. When George fell ill, Jonathan found a letter from Dio's father, Dario, and realized that Dio was poisoning his father to steal the Joestar family fortune. Though he had no physical proof other than Dio's clear animosity towards his biological father, Jonathan left his own in the care of physicians while attempting to find an antidote. Jonathan's search takes him to Ogre Street, where he manages to win over the friendship of a local thug named Robert E. O. Speedwagon, who had attempted to mug him before realizing the kind of person he was. With Speedwagon's help, Jonathan finds Dio's poison supplier, Wang Chan, and obtains the antidote for his father.
Dio arrives at the estate and sees Jonathan, Speedwagon and George waiting for him along with constables to take him away for attempted murder. Dio, having learned the power of the Stone Mask, attempts to kill Jonathan and use his blood to transcend humanity and become an immortal Vampire. George takes the stab wound meant for Jonathan, prompting the constables to open fire on Dio, supposedly killing him. As Jonathan laments, Dio is revealed to be alive and uses his new vampiric state to incapacitate Speedwagon and slaughter the constables. Noting Dio's newly gained regeneration, Jonathan is forced to set fire to his home in hopes that the amassed heat would kill him. After a long struggle, Jonathan plummets Dio into the inferno and impales him on a statue of the goddess Venus, effectively trapping him in the flaming building. As Dio curses him, Jonathan is blasted outside the manor by an explosion and is remains alive despite many burns and injuries. Speedwagon manages to take Jonathan to a hospital, where the protagonist ends up seeing Erina for the first time in seven years. Despite Dio's actions in the past, it did not change Erina's feelings for Jonathan as she nursed him back to health.
After being discharged from the hospital a few days later, Jonathan meets William Anthonio Zeppeli, an Italian martial artist trained in the art of Sendō. After completely healing Jonathan's body, Zeppeli reveals that Dio survived the estate burning and offers to teach Jonathan to utilize a respiratory-based solar energy called Ripple in order to defeat Dio and destroy the Stone Mask. After a time of training, Jonathan learns from Speedwagon that Dio had apparently set up base at Windknight's Lot, resulting in the disappearance of several of its citizens. Drawing near to the village, the group is attacked by a newly zombified Jack the Ripper sent by Dio. Zeppeli offers the zombie's defeat as a final test for Jonathan, giving him glass of wine and ordering him to defeat Jack without spilling a drop. Jonathan eventually realizes he can use the glass to detect Jack before defeating him by transmitting Ripple through the wall. Once at Windknight's Lot, Jonathan and his group are unknowingly led by a hypnotized boy named Poco to a graveyard where Dio's large number of minions ambush them the moment night falls.
Dio reveals himself at that time, having learned of the Ripple fighting style and uses his flash-freeze ability to render bare-handed attacks with Ripple useless. Dio then reveals his strongest zombie warriors, the knights Bruford and Tarkus. Bruford senses Jonathan's fighting nobility, requesting Dio to let him fight the human in a duel. Taking their battle underwater, Jonathan is at a disadvantage as he is unable to maintain proper breathing and thus is unable to use Ripple. Recalling a lesson from his late father, Jonathan dives deeper into the water where he finds air bubbles trapped underneath rocks; using these to breath, Jonathan is able to generate enough Ripple to force Bruford out of the water. Bruford tries to finish off Jonathan, but Jonathan channels Ripple through the zombie's sword to literally disarm him before unleashing a flurry of 'Sunlight Yellow Overdrive' punches. As Bruford breaks down, he regains his human soul and in respect for Jonathan leaves him his sword.
After experiencing Tarkus' power, Jonathan and company decide to retreat into a canyon on a leaf-based hang-glider that Jonathan and Zeppeli magnetize with Ripple. Landing within an ancient knight's battleground, Tarkus ambushes the group and manages to trap Jonathan in the "Lair of the Two-Headed Dragon", forcing him into a Chain Neck Deathmatch. Jonathan is nearly killed by the more experienced combatant, but is briefly saved by Zeppeli who ends up sacrificing himself. It is only after the dying Zeppeli infuses Jonathan with his remaining ripple that the youth revives with the strength necessary to defeat Tarkus. Afterwards, Jonathan cremated Zeppeli's body before resuming the search for Dio.
Soon after meeting the Ripple masters Tonpetty, Straizo, and Dire, Jonathan saves Poco's sister from Doobie before confronting 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, livid over Dire's last attack, summons his zombies to take care of the others while he deals with 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 set his fists on fire to remove Dio's advantage and lands a Ripple-infused punch into Dio's stomach while sending him plummeting off the edge of the balcony. Believing Dio dead along with most of his minions, Jonathan's group destroys the Stone Mask.
Two weeks after the Windknight's Lot incident, Jonathan marries Erina and two board a ship heading to America for a honeymoon. During the trip, Jonathan is led to the ship's hull by Wang Chan, where he encounters the embodied head of Dio, whose epiphany of their fates deeply woven together motivated him to take the Joestar's body as his own. Dio then shoots beams of eye humor at Jonathan's throat in an attempt to instantly kill him, but the attack only fatally wounds Jonathan with his stopped breathing preventing him from using his Ripple. Regardless, Dio orders Wang Chan to rip off Jonathan's head while warning him to be both respectful and wary of his new body. Using the last of his Ripple, Jonathan destroys Wang Chan's head and manipulates his body to obstruct a piece of the cruise ship's mechanism. Jonathan intended this to cause an explosion that would sink the ship and hopeful put an end to Dio for good.
While Erina was content to die with him in his final moments, Jonathan beseeches her to escape with an infant whose mother died protecting her from the zombies that Wang Chan sired. Dio makes a last-ditch attempt to take Jonathan's body at that time, only to be stabbed and restrained by Jonathan who felt at peace in his final moments. Dio attempts to convince Jonathan to let him go with promises of immortality, only to learn that he had already died before the two were consumed in the inferno caused by the ship's explosion. With his death, Jonathan was survived by Erina and their unborn son.
Jonathan's story was known only to a few, namely his son George Joestar II and later his grandson Joseph Joestar and his descendants. Despite Jonathan's last act, Dio manages to take the headless body of his rival for his own and resurfaces from the ocean depths a century later. Once freed, the renamed DIO uses Jonathan's body to impregnate a few women: resulting in the births of Giorno Giovanna, Donatello Versus, Ungalo, and Rikiel. DIO then pierces his new body with the Bow and Arrow, awakening the ability to use a Stand. DIO also gave Enrico Pucci one of Jonathan's finger bones to enact his dream of 'ascending to Heaven'.
During the events of Stardust Crusaders, DIO decides to completely integrate Jonathan's body to perfect his Stand by using Joseph's blood as a catalyst, but ends up being utterly defeated by Jonathan's great-great-grandson, Jotaro Kujo. After DIO's death by Jotaro's hand, he and Joseph expose what remained of Jonathan's body to the sun as an apparent end to their feud with DIO, allowing Jonathan to rest in peace.
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.