Jonathan Joestar was born on April 4, 1868 to George and Mary Joestar, two Lowlander Scot aristocrats who were quite happily married. Tragedy struck soon after, for when George, Mary, and Jonathan were returning from an auction, where Mary won a mysterious Stone Mask of Aztec origin, their carriage slipped in the mud and fell down a cliff. Mary was killed instantly, having sacrificed herself to protect baby Jonathan, while George was grievously injured. George was "saved" by a conman and thief by the name of Dario Brando, who was actually looking to loot the seemingly dead George's belongings and body parts. George, grateful for the questionable services the man provided, promised to help him whenever he needed it. For twelve years, Jonathan was raised by his father in their country manner, and he was happy and healthy with a group of friends and a loyal dog named Danny.
However, this period of bucolic tranquility came to an end when a new member of the household arrived, Dio Brando. Dio was the son of Dario, who had died just recently, and Dario had asked George to raise Dio as his own and help him realize his potential, a request George gladly accepted. Dio was handsome, charismatic, and talented at whatever he did, seemingly the perfect aristocratic son. However, from the beginning he had a dark ambition to climb to the top using whatever means and whoever he could. To this end, he sought to isolate the young Jonathan and break him so that he may take his place as the inheritor of the Joestar fortune. To this end, he split Jonathan and his girlfriend Erina, who helped Jonathan when he was isolated from his friends, and after Jonathan angrily retaliated, he brutally murdered Danny. After this incident, when Jonathan didn't break, Dio stopped acting against him for 7 years. During this time, the two developed a cordial relationship, though neither could truly accept the other, for Jonathan could not forgive Dio for what he had done, and Dio was merely biding his time.
When the two were graduating college, George Joestar had suddenly fallen ill, complaining of chest pains, swollen feet, and a cough. Dio was personally delivering his medicines, and he protested taking George to a hospital, claiming they only cared about money and not healing. Little did George and Jonathan know, Dio was in fact poisoning the former with Asian medicine he had received from a peddler by the name of Wang Chan in London's Ogre Street. Jonathan managed to connect the dots during a late night study session, finding a letter from Dario Brando to George Joestar complaining of the same symptoms, and he confronted Dio about it, managing to bait him into confirming his suspicions. When the college couldn't identify the poison, Jonathan headed out to Ogre Street to get it identified by the Asian medicine peddler. When he got there, he was attacked by a thug by the name of Robert E.O. Speedwagon and his goons, but he quickly defeated them. Impressed with his strength, courage, and kindness, Speedwagon took him to Wang Chan, who promptly identified the medicine and agreed to come back with them with an antidote.
They then set an ambush with the police at Joestar manor, where they managed to catch Dio coming back. Dio, to everyone's surprise, didn't fight tooth and nail, but instead surrendered with the condition that Jonathan be the one to handcuff him. As Jonathan prepared to do so, Dio immediately attempted to stab him with a knife, but to everyone's horror, George Joestar took the attack instead. Dio then used his blood to activate the Stone Mask and immediately turned into a vampire, killing all the cops present. Jonathan, in an attempt to fight the monster, burned his house down and pinned Dio to the Goddess of Love statue in the entryway, hoping the flames would stop his regeneration, getting all his limbs shattered in the process.
He then spent a few weeks recovering, tended to by a now grown up Erina Pendleton, who had become a nurse. They rekindled their relationship, and Jonathan's recovery progressed well. Eventually, when he was well enough to walk, they went out and were met by a strange man who introduced himself as Baron Zeppeli. The man demonstrated superhuman speed, and he jabbed Jonathan in the diaphragm with his pinkie, causing a strange energy to flow through Jonathan's arm, healing it. Baron Zeppeli then informed Jonathan the mask was still out there, as was Dio, and he needed to train in an art called Hamon in order to stop him. Jonathan agreed, and they trained for about a week, at the end of which Speedwagon came and informed them that Dio had set up a base in the town of Windknight's Lot. As soon as they entered the town, they were attacked by Jack the Ripper, at this point a zombie servant of Dio, and Jonathan defeated him for his final exam, learning how to track enemies using Hamon. Soon after, they attacked and were overpowered by Dio, who left his elite servants, the knights Tarkus and Bruford, to deal with them. Bruford still possessed a sense of honor, though it was warped into a love of killing, and demanded single combat with Jonathan as a "warm-up". After an intense battle, Jonathan pumped him full of Hamon. This restored his humanity and the honorable knight Bruford was in life, and in gratitude, Bruford gifted Jonathan his beloved sword given to him by his Queen, Luck, and added a new name with his blood, Pluck. Tarkus attacked soon after, and Jonathan found himself trapped in a Chain Jail Tournament, and his Hamon was cut off. Zeppeli attempted to help him, but Tarkus cruelly bisected the Baron and broke Jonathan's neck. Jonathan was still alive, and Zeppeli wasted no time giving him all the Hamon he had left, which gave Jonathan the power he needed to break free of his collar and decisively defeat Tarkus. After a short mourning period, he moved on.
Soon after, he met up with Zeppeli's Master, Tonpetty, as well as some comrades Zeppeli had called for help, and together, they advanced on Dio's castle. Jonathan and Dio eventually engaged in a climactic battle on the parapet of the castle, in which Luck and Pluck was chipped, though not before it helped Jonathan find a way around Dio's freezing touch. Dio was launched off the parapet, his body attacked by the Hamon of Jonathan's final blow, and the group called it a day, destroying the Stone Mask.
A few months later, Jonathan married Erina at last, and the two prepared to set off to America on their honeymoon. However, Dio had survived the battle, and his disembodied head was stowed in a coffin on the same ship the newlyweds were taking, intent on stealing Jonathan's body out of some twisted admiration. After zombifying most of the ship's crew and passengers, Dio managed to lure Jonathan below deck and puncture his windpipe, cutting off his Hamon and mortally wounding him. Not one to give up, Jonathan used the last of his Hamon to manipulate Wang Chan's body to stop the boat's screwshaft, building up pressure and causing it to explode, stopping Dio from spreading his reign to America. Fortunately, Erina managed to escape alongside a little baby using Dio's coffin, and both were eventually picked up in the Canary Islands, where Erina and Jonathan's son George II was born. Jonathan himself expired in the burning boat embracing Dio's head, and his journey ended at last. Or so it seemed.
When Dio stole his body, the former was aware Jonathan's soul was dormant within it, especially when he awakened two Stands, The World and a Hermit Purple Stand. What he wasn't quite aware of is that Jonathan was still conscious of what was happening around him and what Dio was doing with their now shared body. He became aware of Dio's plan to achieve Heaven, he was forced to witness Dio use his body to impregnate 4 women as well as suck many others dry for sustenance, and both of them had to adjust to a much changed world. Of particular importance to Dio's plan was that he discovered the existence of a wish-granting object, the Holy Grail, and he incorporated the Grail into his plan to evolve his Stand to achieve Heaven, learning as much as he could about the ritual known as the Holy Grail War. Jonathan could only gasp in horror when the Stardust Crusaders finally challenged Dio, and he was forced to watch Dio send minion after minion in their way and later personally kill Kakyoin and Joseph. He finally died when Jotaro defeated DIO, but he could not go gently, for he knew Dio's plan had not died with him, and he swore that until the day Dio's plans were ended once and for all, he would never pass on to the Throne, and he made a contract with Alaya for that purpose.