The sixth part of JoJo’s Bizarre Adventure, Stone Ocean, reintroduces Jotaro Kujo as something of a villain. Jotaro isn’t depicted as suddenly being evil in any way, nor is he antagonistic to any of the characters. Rather, he can be considered a villain largely due to his past actions, or lack thereof, causing the plot to happen the way it does.
Chronologically, Jotaro’s appearance in Stone Ocean is a little over twenty years past his first appearance in Stardust Crusaders, and in that time, his character has mostly stayed the same. Jotaro was originally introduced as a strong, stoic man who kept to himself and rarely expressed himself outside of when he was angry. That characterization has largely stayed the same as he reappears in Stone Ocean, in addition to his reappearance in Diamond is Unbreakable and brief role in part five, Golden Wind. The lack of major development of Jotaro’s part is due to him largely being a static character, meaning the way he’s written at the start of the story is more or less how he’ll be until the end. For the most part, Jotaro being the way he is had never been a problem since the story had never been structured in a way that would strongly react to his character.
All of that changed with Stone Ocean. Through means of deconstruction and applying a bit of realism, Jotaro becomes something of a villain. Realistically speaking, someone, as closed off as part three’s Jotaro, would have difficulty building and maintaining relationships with other people, especially if those people were family, and that’s exactly what happened with his own. The aspects of Jotaro’s personality that made him a strong character in earlier parts made it difficult for him to maintain meaningful relationships with his family. As a result, he and his wife divorced, and his relationship with his daughter, Jolyne, became increasingly strained.
Because Jotaro was as bad as he was at expressing himself, Jolyne grew up feeling unloved by her father; something further emphasized in her mind by him always being out of the country for work. The lack of love from her father caused her to fall into a life of delinquency out of a need for attention, something the manga even explicitly states at one point. Thanks to that, Stone Ocean‘s Jolyne slowly evolved into the kind of person who could be manipulated by the newest antagonist, Enrico Pucci, which led to all of the events of Stone Ocean happening.
In a way, Jotaro is responsible for the events that transpired in Stone Ocean because his bad parenting started a domino effect that resulted in Jolyne being manipulated and, concurrently, the events of the story as a whole. In that regard, Jotaro can be interpreted as a villain of part six, if only because of the effect his character has on the story. None of Jotaro’s actions make him evil or antagonistic, especially since he didn’t go out of his way to do them, but the fact still stands that the latest installment of JoJo’s Bizarre Adventure paints Jotaro’s character in a negative light.