With help from the treasure hunter Jon, Musashi finds the Earth Scroll and defeats its crest guardian. After its defeat, half-vampire and half-zombie creatures known as Vambees appear in the nearby village. While searching for a way to stop the Vambees, Musashi finds the Water Scroll and defeats its crest guardian in the basement where the Vambees originate. While Musashi searches for the Fire Scroll, Musashi's rival, Kojiro, kidnaps Princess Fillet and uses her as a hostage to force a battle with Musashi. Kojiro is defeated and Fillet is then rescued. Musashi then searches for thieves from the Thirstquencher Empire and makes his way to the next crest guardian. It is then revealed that Princess Fillet is actually one of Thirstquencher's thieves disguised and that the real Fillet is still in their hands. Musashi then continues his journey, finds the Wind Scroll, and defeats its crest guardian in an ants' nest.

After finding the fifth and final Scroll, the Sky Scroll, Musashi discovers Thirstquencher's base, a floating ship known as the Soda Fountain. Musashi attacks the base and defeats the Sky Guardian. Thirstquencher's leader, Flatski, forces Musashi to give him Lumina in exchange for the Princess, and frees the Sky Crest. However, this unleashes the Wizard of Darkness, who was sealed within Brave Fencer Musashi's sword Lumina the entire time. It is also revealed by Jon that the original Brave Fencer Musashi sealed The Dark Wizard within the sword. Furthermore, it was Brave Fencer Musashi who entrusted the crests to the crest guardians to prevent The Dark Wizard's seal within Lumina from being broken. In effect, the present Musashi's quest merely aided The Dark Wizard's revival. Musashi recovers Lumina and uses it to defeat The Dark Wizard. After returning the Princess to Allucaneet Kingdom, Musashi takes Lumina to the place where he found it.

While the game conceptualized as an action oriented, Musashi was originally meant to be a wanderer. However, he was later changed to an itinerant Samaritan in order to have him interacting and helping other characters. During development, the team used an action base which was crucial to the game's fighting mechanics. Director Yoichi Yoshimoto was focused on the game's fully polygonal aspects that were a departure from Square's previous works. The development team prioritized the movement of polygons in real time and how light affected their appearance.^[7]

When developing the characters for the game, Sakaguchi did not have a positive opinion of how popular the game would become. However, after the staff designed the graphics and the gameplay, he was surprised by the work, commenting that it was more interesting.^[6] The characters were designed by Koji Matsuoka and illustrated by Tetsuya Nomura. When the game was localized（英语：Video game localization） for an English release, translators had to change alcohol-based names with soda-pop names due to problems with rating boards. This resulted in several jokes being lost in translation.^[8] The game's English title was changed from "Brave Fencer Musashiden" to "Brave Fencer Musashi" in order to avoid confusing non-Japanese players about the titular character's name, as "Musashiden" means Musashi's story.^[9]