The original six-episode series in 1993 begins with Jotaro, Joseph, Avdol, Kakyoin, and Polnareff in the Egyptian desert on their quest to find DIO (Volume 20 in the manga). The series offers very little exposition, assuming the viewer is already familiar with the backstory and first half of Stardust Crusaders. A prequel seven-episode series was released in 2000, offering an explanation for those unfamiliar with the story in the previous series. It starts at the beginning of Stardust Crusaders with Joseph arriving at Japan to explain Jotaro's strange behavior (Volume 13 in the manga).
The entire 6-volume (13-episode) anime series released in English from 2003 to 2005 in canonical order by Super Techno Arts.
Jotaro learns the secret of his Stand power and about his family's enemy, the vampire DIO. Later, Jotaro is attacked by “Hierophant Green,” an enemy Stand controlled by DIO's assassin, Noriaki Kakyoin, who is under DIO's control. When Holy falls into a Stand-induced coma, Joseph, Jotaro and the others embark on a dangerous journey to Egypt to save her life and end the 100-year battle between DIO and the Joestar family!
When the private jet carrying Jotaro and his companions to Egypt suddenly bursts into flames, the plane is forced to land in the ocean. As the party drifts in a lifeboat, a large freighter pulls alongside and they climb aboard. To their shock, there is no crew to be found—and the only passengers left aboard are an Orangutan and enemy Stand user Jean Pierre Polnareff.
At a stopover on the way to Egypt, Polnareff is attacked by "The Hanged Man," an enemy Stand who has two right hands and can only be seen in reflections. Realizing that it must be controlled by the same Stand user that had killed his younger sister, Polnareff breaks away from the rest of the group to seek his revenge. Polnareff is lured into a trap set by The Hanged Man and his partner, Hol Horse. When some of the party come to his aid, one is killed by Hol Horse's Stand, "The Emperor."
Kakyoin and Polnareff desperately seek a way to defeat The Hanged Man, who can strike out at them from "the world inside the mirror" while remaining invulnerable to their attacks. How can they hope to defeat an enemy who can move at nearly the speed of light and attack from almost any direction?
A thick fog envelopes the group as they travel towards Egypt, so they seek refuge in a nearby town. There, the companions stumble across a strangely mutilated dead body lying on a street corner. An old woman arrives on the scene with the police, and offers to let them stay at her hotel for the night. In the hotel bar, Polnareff encounters Enya, a beautiful and mysterious young woman on a deadly quest of her own.
Polnareff becomes a living puppet under the control of N-Yah and her incredible Mist of Death Stand, "Justice." The group battles its way out of the hotel, only to find themselves surrounded by legions of the dead. All seems lost when Jotaro falls prey to a bizarre sneak attack, leaving him vulnerable to N-Yah's control as well.
Jotaro and his companions finally reach Egypt. There, they are met by a Speedwagon Foundation helicopter that delivers a new addition to their group—the mysterious Iggy "The Fool." When the helicopter crashes just a short time later, the group investigates, only to find themselves pitted against another of DIO's assassins—N'Doul and his deadly Stand, "Geb."
Jotaro and the others find themselves stranded and at the mercy of N'Doul's incredibly strong and mercurial Stand, "Geb." Faced with almost certain death, Jotaro makes a desperate gambit and forces Iggy to help him strike back at N'Doul, but Iggy has other plans. He betrays Jotaro at a critical moment, offering him to "Geb" in order to save his own life.
The companions search the huge Egyptian capital of Cairo, showing everyone they meet the photo of a mysterious building where they think DIO resides. In an odd cafe, they encounter a gambler named D'Arby who claims to have the information they need. The catch is, they have to beat him in the ultimate wager—one where their very souls are at stake! Can the Joestar party outwit a master gambler at his own game?
Jotaro and his companions finally arrive at DIO's lair and find their way to the room where his coffin resides. Just as they prepare to strike the fatal blow, DIO's mysterious Stand powers, coupled with that of his finest assassin, Vanilla Ice, slay one of the party before the group's horrified eyes. But even that doesn't quench DIO's thirst for blood...
DIO pursues Joseph through the streets of Cairo, leaving an incredible swath of death and destruction in his wake. Another of the companions comes to Joseph's aid, only to be crushed by the power of DIO's Stand, "The World." As the shattered hero lies alone and dying, he realizes in the last moments of life the true nature of DIO's Stand... can he warn the others before it's too late?
Jotaro and DIO. "The World" seems invincible as Jotaro is struck time and time again with murderous blows. If Jotaro cannot discover the secret of DIO's Stand and find some way to counter it, the Joestar line will come to an abrupt and bloody end.
The story of Part 3 was largely omitted; the majority of Stand battles from the manga are removed in the OVAs.
In the OVAs, Enya can use Justice to transform herself into an attractive young woman. In addition, the flesh bud that kills her is not triggered by Steely Dan.
In the manga, after Jotaro is freed from jail, he, Joseph, Avdol, and Holy discuss DIO's whereabouts at a cafe. In the OVA, they discuss DIO's location at Holy's house.
In the manga, Jotaro fights Kakyoin in the school infirmary. In the OVA, they fight in a nearby forest. In addition, the subject possessed by Hierophant Green has been changed from the school doctor to a female student.
The group doesn't meet Polnareff in Hong Kong like in the manga. Instead, they meet him inside Strength. In addition, Polnareff was not controlled by one of DIO's flesh bud parasites.
In the manga, Jotaro defeats Forever by pummeling him with Star Platinum. In the OVA, Forever is instead sliced in half by Polnareff's Silver Chariot.
The group's visit to Singapore is completely removed.
After D'Arby is defeated, he gives away the location of DIO's mansion, but goes completely insane before he can reveal the secret of DIO's Stand; in the manga, he goes insane before he can reveal either piece of information.
Kakyoin does not rejoin the group before they enter DIO's mansion. Instead, he arrives just in time to save Joseph from DIO.
Nukesaku is omitted from the story, causing the scene where DIO's coffin is opened to be significantly different: The protagonists find it on their own, only to find Avdol inside when he opens it with Magician's Red. DIO appears before everyone on one side of the room and congratulates them for their efforts, before warning that someone is coming for them. Avdol then pushes Polnareff and Iggy away, at which point he is instantly killed by Cream.
Much of the battle with Vanilla Ice is cut in the OVA. Iggy dies by having his lower body erased by Cream, and then kicked and beaten by Ice rather than simply dying of blood loss from a beating.
Vanilla Ice's death is changed as well. Rather than exposing him to the sun, Polnareff kills Ice by stabbing him rapidly and slicing his head in two.
The fight between Jotaro and DIO is changed drastically. In the manga, DIO figures out Jotaro can move in stopped time when he sees his fingers twitching. In the OVA, he finds out when Jotaro survives being punched by The World in stopped time. Their battle also demonstrates extra scenes involving pure physical action as the two wreak havoc on the city of Cairo, with a number of civilian casualties on DIO's part.
DIO drops an oil tanker on Jotaro instead of a road roller, jumping off when it explodes.
Joseph does not pretend to be DIO when revived in the OVA, nor does Jotaro quiz him with questions about movies or music. His revival happens off-screen.
In the OVA, DIO's ashes are dropped and scattered from a plane of the Speedwagon Foundation above the sea instead of being exposed to sunlight at ground level towards the Sahara desert.
Joseph puts on a Gipsy Kings tape in the OVA while in the manga he puts on "Get Back" by The Beatles.
In May 2008, both Studio A.P.P.P. and Shueisha halted OVA/manga shipments of JoJo's Bizarre Adventure after a complaint had been launched against them from EgyptianIslamic fundamentalists, after noticing a scene in the OVAs that had the villain, DIO, reading a book depicting pages from the Qur'an. This recall affected the English-language release of the manga as well, causing Viz Media and Shueisha to cease publication for a year. Even though the manga did not feature that specific scene, Shueisha had Araki redraw scenes that depicted characters fighting on top of, and destroying, mosques. Viz resumed publication a year later, with the eleventh volume being published on April 7, 2009, though distribution of the OVA had been permanently cancelled.
The controversy was such that the Japanese Ministry of Foreign Affairs addressed the issue in an official report about this incident.