The player controls the protagonists of Stardust Crusaders in a combination of Point and click adventure and classic third-person RPG. It is sometimes also referred to as a "side-scrolling RPG." The game makes use of a "biorhythm system" whereby characters' parameters can change if they become stressed. Combat takes place in the usual RPG fashion, with a list of commands and is thus a turn-based RPG. Prior to a battle, the player selects one of the face-down cards offered through DIO's prediction and characters' abilities will change depending on which ones have been chosen.
Commands include the standard "Use" and "Investigate" options, the latter of which also provides a character's insight on the item/situation. In battle, "Attack" deals damage to HP, while the "Talk" command can both damage enemies' "strength of will" and heal allies' (the higher the "strength of will", the stronger the character's attacks are) and said "will" takes the form of MP (mental points). Similar to HP, the character is unable to fight if their MP reaches 0. The "Prediction" command is used in conjunction with a set of tarot cards and tells the character's lucky item. By equipping the item, the effects of the "biorhythm system" are accelerated (unfortunately, if Avdol is not in the party, the command cannot be used). "Tactics" will enable characters to patiently wait a turn (but are open to attacks if possible during such a standby phase) which can open a new set of commands which occur sooner for some characters, and can enable an "Idea" (during certain battles, events are re-enacted from the manga) which has differing effects on the situation at hand, use a "Guts" special attack that deals more damage than normal attacks, or choose to flee from some battles if possible.
The storyline used deviates somewhat from its source, likely due to system limitations.
- "Dollars" are always used as currency, regardless of the country.
- Members of the Speedwagon Foundation appear more frequently to provide clues and money for the heroes (if they sacrifice a day of their trip to rest).
- Joseph routinely uses his Stand on TVs found throughout their journey in order to locate DIO. During these scenes, DIO can see and talk with the entire party. In the original story, he is only seen doing this once.
- Vampires and zombies randomly attack the team in "dungeons" (they were originally scarce in Part 3). The few instances of Joseph's Ripple are absent from the game.
- The runaway girl (Anne) is completely removed from the game.
- Tower of Gray appears in a school and Gray Fly is the school janitor.
- The scene where Star Platinum sketches the fly in the photograph of DIO that Hermit Purple created was removed.
- Polnareff first appears as a shop-clerk in a Japanese bookstore. Joseph suggests going there to find a book about DIO and Stands; in the original story, this information is passed through word of mouth by Stand users.
- Forever's Stand Strength takes the form of a mansion instead of a boat, and is also in Japan; the fight takes place before Jotaro and allies even depart.
- Dark Blue Moon attacks the party within a water trap inside a sewer route found in said mansion.
- After Devo the Cursed's death, Rubber Soul takes on his appearance (in the original manga, he takes on Kakyoin's appearance).
- Empress does not appear.
- Death Thirteen attacks from inside a plane en route to India.
- Midler is a stewardess on the same plane, and her Stand takes on the shape of the restroom's doorknob instead of a mug of coffee in the would-be submarine.
- Steely Dan doesn't appear, though he is mentioned in the instruction manual. The Lovers, subsequently, isn't his Stand, but some sort of seed.
- Enya the Hag is responsible for putting The Lovers into Joseph's head. Due to Steely Dan's removal from the game, Star Platinum and Magician's Red enter Joseph's brain along with Hierophant Green and Silver Chariot (in the original manga, it is only Hierophant Green and Silver Chariot who enter).
- Aside from J. Geil, Hol Horse partners with Mariah instead of Boingo.
- Oingo and Boingo are reduced to a supporting role and do not use their respective Stands.
- Iggy appears at a pyramid in the desert. The part with Geb was almost entirely removed.
- Alessi transforms Kakyoin, Joseph, and Avdol into children (in the original manga, he only transforms Jotaro and Polnareff). He also attacks them within a library, being supported by the Oingo Boingo brothers.
- Wheel of Fortune has a more minor role but is still an opponent.
- Jotaro's group obtain Anubis' sword from a strongbox in a pyramid. Khan is a merchant rather than a barber and negotiates with them to buy the sword. When they refuse, he steals it.
- Chaka is a weapons dealer. He asks to take a look at the Anubis sword and is subsequently manipulated by it into attacking. Anubis is only used twice, but still maintains the same level of power.
- Chaka and Khan's order of appearance is also reversed (in relation to the original manga).
- Daniel J. D'Arby still plays cards but wins by playing normally. His entire scene is scripted as well; In order of Polnareff, Kakyoin, Avdol, Joseph, and Jotaro, the group plays him, losing without fail until it is Jotaro's turn, wherein he will win automatically.
- Telence T. D'Arby battles normally as if his Stand was a power type (instead of betting and playing minigames).
- Vanilla Ice is beaten normally (rather than being destroyed due to sunlight).
- Nukesaku doesn't appear; DIO is already waiting for the main party.
- Jotaro gains the ability to move through stopped time only after he wears a special school uniform for it found in DIO's mansion (in the original manga, he does this naturally).
- Kakyoin, Avdol, and Iggy do not die and instead survive with the rest of the group at the end.
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