Five years prior to the events of STC, on top of Mount Hotaka, Musashi's sensei taught Joe vital techniques such as karate, kendo, archery and horse-riding, all on top of being able to survive against his many potential enemies. The old man taught Musashi many little tricks which would come in handy when his girlfriend Naoko was stolen from him. Around this time, Musashi's sensei was poisoned to death by the Neo Zeed, instilling Musashi with a vengeance. However, he had sworn not to kill anyone, so he used this determination to find Naoko at any cost.
After battling an unknown attacker in a warehouse, his first real lead took him to the Ibakari Province, where a Neo Zeed stronghold was believed to be holding Naoko. Already, Musashi exhibited many strengths like wall-climbing and herbal weapons (he put a dog to sleep with a dart), while remaining completely silent. Climbing the ornamental pagoda, Musashi crept into the pavilion and demanded the whereabouts of his girl, all while never underestimating his foes. Overcoming four attackers at once, Musashi was sent further downstairs to his goal, where he progressively faced tougher opponents who blocked his way. Musashi had to combine skill, strategy and bravery to enter the final room which seemed to Naoko. While he originally believed this to be the case, he soon noticed it was just Water of The Four Elements that had fooled him. Musashi escaped to live another day.
Musashi moved to Tokyo and adopted a disguise in order to scout out the Neo Zeed HQ. Determining that the front was too hard to break into, Musashi opted to fly to the top with a glider and abseiled down the building. Inside, Musashi showed further skill while hacking into a computer terminal, but failed to realise that the enemy would be expecting an unauthorised entry, leading him to be chased by guards. Joe easily dealt with a guard holding a gun and entered an open elevator shaft, using the cable to rappel down. However, the ninja henchmen did not wish to fight Musashi face to face and decided to cut the cable he was travelling down. Skill and a bit of luck helped him escape and he soon stole the disguise of Kenjei, an inept guard. Musashi was soon tricked into entering a death obstacle course, forcing him to navigate a spike trap and flamethrowers, only to be knocked out by heavy nervy gas. The "corpse" of Musashi was taken to The Void and shown to Naoko, only for Musashi to wake up and steal Naoko back from the building.Some time later, Musashi returned to Tokyo to seek out the Four Elements, now working for the Yakuza. Musashi continued to act as a news vendor but was captured by Air. The Shinobi managed to escape the casino he was held in and escaped to the land of the Roofworlders, who allowed him to stay in exchange for security in the event that the Yakuza would come looking for him. They did arrive but the combined efforts of Musashi and Kotomi-sensei proved too strong for them. The Elements returned, this time much more of a threat, but Musashi eventually managed to overcome his strongest enemies, personally steering Air into a brick wall.
As a ninja, Musashi has the ability to appear invisible to a normal man whenever he wants, simply keeping out of sight. Furthermore, he can use haragei to identify the location of threats and prana to either appear dead or draw power from the Earth. Under the tutelage of Musashi's sensei, Joe was able to learn various martial arts and gained survival instincts useful in the next five years. As well as the traditional ways, Musashi was able to hack into a computer and created a perfect disguise that allowed him to slip into modern society perfectly.
Mentally, Musashi can come up with many strategies that can aid his goal, whether it attacking or evading an enemy. In the pagoda, Musashi had to change his plan depending on the current villain, managing to fool the "Monkey King" into defeat and forced a man on stilts to tell him where to go next. Musashi used prana to block the advances of The Void and used medicinal magic to heal Kotomi-sensei.
Shinobi wears a traditional white ninja outfit that would make him stand out terribly where he not trained in keeping hidden. By his second adventure, the white disguise was complimented with touches of red that added flair as well as defense by way of vambraces. Musashi also had an "old man" disguise which he used as a news vendor; this mask and hat could easily be removed every night and replaced the next day.