In 1989, Joseph Joestar arrives in Japan to meet his troubled grandson Joutarou Kuujou at the request of his daughter Holly. Joutarou has locked himself in a jail cell out of fear that an evil spirit is possessing him and that he may cause harm to others. However, Joseph reveals the truth to Joutarou: this "spirit" is really a "Stand," a physical manifestation of one's fighting spirit. What's more, Joseph and his companion Mohammed Avdol possess Stands of their own and have learned to control them with ease.

Joseph's arrival comes with another piece of news: an old family enemy has returned from the grave, causing the Stands of the Joestar family to awaken. However, when a Stand manifests within Holly, her inability to cope with it leaves her gravely ill, stirring the men into action.

Armed with the power of Stands, a globe-trotting adventure from Japan to Egypt—where their adversary resides—begins. Meeting an array of nefarious Stand users along the way, as well as new allies, the team leads a crusade to save Holly and put an end to their enemy for good.

A 17-volume kanzenban version dubbed as JoJonium was published in Japan from December 4, 2013, to March 4, 2015. This edition covered the first three parts of the Jojo no Kimyou na Bouken series and included new cover art which showed redesigns of the characters by Araki Hirohiko. JoJonium's volumes 8-17 cover the third part.

JoJo no Kimyou na Bouken Part 3: Stardust Crusaders was published in English by VIZ Media from November 8th, 2005, to December 7th, 2010 under the title JoJo's Bizarre Adventure. It was not labeled as Part 3 until later; this was due to it being the first of the series to be published in English. The publisher has published the series uncensored following the JoJonium format and content from November 1, 2016 to February 5, 2019. It was also published in Italian by Star Comics from March 1995 to March 1997.

Several minor changes were made to the English release, apart from changes to several copyrighted stand users names and violence to animals and children being changed, an online group of Muslim protesters halted the release of the manga for a year. This was due to a scene in the OVA where the antagonist, Dio Brando is seen reading pages from the Qu'ran—which was not even present in the manga. Shueisha requested many scenes featuring fighting which involved buildings resembling mosques be redrawn.