Jotaro is the son of Miyamoto Usagi, but due to circumstances they do not acknowledge it and treat each other as uncle and nephew. However, many people have noted their strong similarities to each other. Jotaro is currently training to be a samurai under Katsuichi.
Jotaro is the son of Kenichi and Mariko, but his real father is Usagi. Before leaving to serve Lord Mifune, Usagi had a tryst with his childhood love, Mariko, which led to them conceiving Jotaro. Mariko later discovered she was pregnant. Kenichi, who was also in love with Mariko, convinced her to marry him, so that she would not be dishonored by having a child out of wedlock. Kenichi treated Jotaro as his own child, and genuinely loves as if he were, but it is one of the many sticking points between Kenichi and Usagi. For years, Usagi never knew that he had fathered a child, and Mariko refused to tell him so as to not make him feel obliged to resign his post and return to her. Then came the Battle of Adachi Plains and everyone believed that Usagi had died with his lord.
Jotaro first met Usagi in the issue "Homecoming!". Usagi was returning to his home village to pay respect to his late father's grave, but at the time the village was being besieged by Mogura (Mole) Ninjas. Usagi crossed paths with the mole ninjas as they were stealing the village's winter rations and had taken Jotaro hostage. The ninjas thought Usagi was one of the villagers come to stop them and attacked, Usagi killed one of the ninjas and saved Jotaro, and the mole ninjas were forced to retreat when the villagers came rushing at them. Later that night, the Mole Ninjas burrowed under the house and tried to take Jotaro hostage again as retaliation, but Jotaro bit his attacker on the hand which gave Usagi the opportunity to kill the ninja. Usagi complimented the boy for his courage. Usagi departed from the village after he paid his respects to his father's grave.
Jotaro later appeared in the issue "Circles". Weary of his travels on the road, Usagi decided to return home to his village to stay for good. First, he decided to pay his respects to his teacher Katsuichi. At the same time, bandits were again plaguing the village, and they were being led by the demon spearman Jei who claimed that the gods had guided him here and was using the bandits as tools to carry out their will. While Jotaro was out collecting mushrooms, Jei came across the boy and kidnapped him, sensing in him some connection to the long-eared ronin he had set out to kill. Usagi learned of Jotaro's disappearance and gave his assistance to Kenichi.
Jotaro was taken to the bandits' hideout, and though the other bandits wanted to get rid of the boy, Jei made it clear Jotaro was under his protection, at least until the long-eared ronin showed up. While he was captured, Jotaro befriended a tokage lizard he had given some of his food to, and the tokage helped Jotaro by chewing on the ropes holding. Usagi and the others managed to find the bandit's hideout and launched an attack, and while the bandits were occupied in the fighting, Jotaro made his escape, but he was chased after by Jei. Jotaro fled into the woods and was cut off at a cliffside where he was found by one of the villagers. Jei soon appeared and quickly killed the villager, taking Jotaro hostage once again.
That was when Usagi finally appeared, just as Jei wanted. Knowing that it was him Jei truly wanted, Usagi demanded that he let the boy go, now that he had no further use. Jei refused at first, knowing how much the boy meant to Usagi. It wasn't until Usagi mocked Jei and his gods for being so craven as to hide behind a child that Jei finally released Jotaro. Usagi told the boy to back to his father so he wouldn't distract him during his fight with the demon spearman. Jotaro managed to find Kenichi and told him where Usagai was, which made it possible for Kenichi to save Usagi from falling of the cliff after he had thrown Jei over the side.
Two weeks later, Mariko, who had been avoiding Usagi for most of this time, sent him a message to meet him in a secluded bamboo grove. There, she begged Usagi to leave the village once again. When he asked for an explanation, Mariko finally told Usagi the truth about Jotaro, that he was Usagi's son, not Kenichi's. His whole life, Jotaro only knew Kenichi as his father, who was a good and loving father to him, and Mariko feared that Usagi's presence in the village would alienate Jotaro from Kenichi. Usagi bitterly obliged Mariko.
As Usagi was leaving the village, he was greeted once more by Jotaro, who showed him the tokage lizard that helped him earlier, naming it Spot. As the two walked the road that led to borders of the village, Jotaro spoke of how he wanted to be a samurai one day. Usagi suggested that he seek out the mountain hermit Katsuichi for instruction. The two said their farewells, and Usagi sadly left.
Sometime later, Jotaro did indeed become a student of Katsuichi's, and when the old sensei received a message from Usagi scheduling a meeting with another swordsmaster named Nakamura Koji for a duel, Katsuichi, Jotaro and Katsuichi's other student Shunji, left for Kitanoji Temple. As they made their way to the appointed place and time, their paths crossed with both Usagi and Koji when they happened upon a village that was being plagued by bandits and decided to help them. When Koji and Usagi went into the nearby mountains to scout the bandits, Jotaro followed after them, and was undetected by the two of them for most of the way. When they did find the bandits encampment, Jotaro, thanks to his small size and sneakiness, was able to slip into the camp unseen and find out the strength and number of the bandits. Koji was impressed with the boy's courage and resourcefulness, and said that he reminded him a lot about Usagi.
Katsuichi came up with a plan to attack the bandits when they were least expecting it. When the fight was against them, the bandit leader tried to flee on a horse and would have escaped if it weren't for Jotaro, who, armed only with a bo staff, knocked the bandit chief right off his horse. The bandit tried to take Jotaro hostage, but Jotaro bit him hard on the hand which distracted the bandit long enough for Koji to land a killing blow. Jotaro hit his head on the ground and blacked out. When he woke up, he apologized to Usagi and the others for not listening and causing trouble. Koji, however, stated that it was thanks to Jotaro that they managed to slay the bandit chief and thus save the village, and complimented that he acted as a true samurai.
Jotaro witnessed Katsuichi and Koji's duel alongside Usagi, which resulted in Koji's death. During the funeral they held for him, Usagi informed Jotaro that Kojij had left his daisho to him when he comes of age after seeing a kindred spirit in him. Jotaro vowed that he would grow up to a be a great samurai like Nakamura Koji; a noble goal according to Katsuichi.
Katsuichi decided that he and Shunji would make a pilgrimage to a temple in the south to pray for Koji, and in the meantime, Jotaro would travel with Usagi. Katsuichi then revealed that he had already deduced that Jotaro was Usagi's son, as the boy was exactly like his father was at that age. They all departed with the intention to meet up again at Kitanoji Temple in a month.
During Jotaro's travels with Usagi, the two shared many adventures together and met many of Usagi's friends. The neko ninja Chizu, the thieves Kitsune and Kyoko, Sasuke the Demon Queller, the Lone Goat and Kid, and Tomoe Ame. They fought gangsters, bandits, ninja, samurai a dark sorcerer and they even ran afoul of Koroshi, the Assassin's guild. During their travels, Jotaro learned many things aside from martial arts from Usagi, most especially, what life as a student warrior is like and what it truly means to be a samurai. And on numerous occasions, many of the people the two encountered commented how Usagi and Jotaro seemed like father and son.
After the month was over, they met back up with Katsuichi so that Jotaro could continue his training, they shared one last adventure when they encountered members of the Assassin's league again. When they arrived back at Kitanoji Temple, Jotaro at last received Nakamura Koji's daisho, and he swore he would try to live up to Koji's legacy. Then the time finally came for them to say their goodbyes, Usagi almost told Jotaro the truth but instead told him that his father was proud of him. They hugged each one last time and said how much they loved each other, and Usagi finally, and bitterly, left. After Usagi's departure, Jotaro revealed to Katsuichi that before he left to study with the mountain hermit, Mariko mother told him the truth about his parentage, During their travels, Jotaro wanted to badly to tell Usagi but realized that he was meant to follow the warrior's road and he couldn't do that with the burden of knowing he had a child. At the last moment, Jotaro ran outside towards Usagi's direction and proclaimed as loud as he could that he is his father; a message that Usagi is too far away to hear.
Jotaro didn't see Usagi again for a while until he came back through the province and ended up back at the village. At the time, the village was being held hostage by Mifune loyalists who were planning on killing an emissary for the Shogun who was on his way to see Lord Hikiji. In order for their plot to work, the loyalists were going to slaughter the village. Mariko managed to escape and found her son and his sensei and brought them back to help Usagi and Kenichi battle their attackers. The loyalists were defeated, and Jotaro was reunited with his family. For a brief time, Jotaro and Usagi spoke together as he was once again leaving the village. Since he still wore the kamon of the Mifune clan, and Hikiji would no doubt hunt any Mifune loyalist down, Usagi had to leave his childhood home once again. They hugged each other one last time and said they loved each other before departing once more.
So far, the only ones who know the truth of Jotaro's parentage outside his family is Katsuichi and Tomoe.
Jotaro is much like Usagi was in his youth: headstrong, brave, eager, adventurous, also hotheaded, impetuous, somewhat naive and emotional. Jotaro has a strong sense of justice and can't stand to see others bullying the weak, and is always ready to spring into action. However, he has a bad habit of acting before he thinks, which has landed him in trouble from time to time. Despite his youth, however, he also shows great maturity in some regards, especially when it came to the matter of telling Usagi about the truth of his parentage. Though he wanted to tell Usagi the truth, he chose not to because he didn't want to take him away from his life.
As a student warrior, Jotaro uses a bokken. Like Usagi, Jotaro is naturally talented when it comes to martial arts even though he has only trained with Katsuichi for a short time. His travels with Usagi expanded his skills at martial arts even further. Despite his small size, he's been able to take on full grown adults, who underestimate him for being a kid, thanks to his speed and being a hard target to hit. His fearlessness often gives him strength beyond his size in battle, as demonstrated when he brought down not only adult men many times stronger than him, but also when he brought down a bandit chief on a horse in full gallop. Often times, he'd brought down his attackers by hitting them in the legs and the groin.
During Part 4 of "The Return", Jotaro demonstrated great improvement with his martial arts training. His archery made the difference in helping both Kenichi and Usagi, and he's now shown to be skilled enough to fight with a live blade.