Shinobi is a series of stories in Sonic the Comic, based on the video game series of the same name. The four strips (five if you include The Official Sonic the Hedgehog Yearbooks) exclusively followed Joe Musashi on his journeys through Japan. The majority of the series showed Musashi look for the love of his life, Naoko, who had been captured by the Neo Zeed, although the final entry focused on Joe attempting to defeat his enemies, The Four Elements.
In Tokyo, Japan, Musashi begins his quest to find Naoko. His travels bring him to a warehouse marked with the symbol for The Void, leader of the Neo Zeed. Inside, Musashi uses his haragei to locate any threats, but he can't detect any. Heading upstairs and considering rumours that the Neo Zeed have developed magic, Musashi is surprised by a cloud of gas and an invisible assailant who knows just where to strike. Musashi stays conscious long enough to spot his enemy and easily defeats him. With a relentless determination, he continues his search elsewhere.
Beginning in Issue 1 of STC, Musashi visits the Ibakari Province of Japan where he believes the Neo Zeed are holding Naoko. Scaling an ornamental pagoda in silence, he makes his way into the building and challenges the foot-soldiers inside, demanding to know Naoko's whereabouts. He soon learns that he has stumbled into a trap, one that must see him defeat several highly-trained Zeed warriors before he can learn more of where Naoko is. After several touch battles, he thinks he has found Naoko, only for it to be Water of the Four Elements. Realising Naoko was never here, Musashi makes a quick exit and lives to fight another day.
Musashi returns to Japan and takes up the position of a news vendor outside the Neo Zeed building, hoping to gain information. He decides the safest course of action is entering from above with a glider and abseils through a window. After hacking a computer terminal, the building is alerted to his presence and guards are hot on his tail. After evading them and heading into an open elevator shaft, he is attacked by ninjas but survives. After taking the place of henchman Kenjei, Musashi is tricked into a death obstacle course and is seemingly killed by heavy nerve gas. He is taken to the room of The Void, prison for Naoko, where Musashi reveals he was really just in a state of prana. Taking Naoko with him, Musashi evades the capture of The Four Elements and completes his quest.
Fresh from his victory, Musashi battles more Neo Zeed ninjas only for him to come face to face with The Void himself in an alleyway. The villain seems to be winning and even destroys Musashi's blade, but the Shinobi uses prana to gain powers of his own and destroys The Void's hand, winning the battle. Not willing to kill him, he orders The Void to return to the Neo Zeed and say he wishes to be left alone.
Musashi returns as a news vendor to stake out the home of the Yakuza, the crime organisation the Four Elements have affiliated with. They discover that Musashi has been watching them and capture him, only for him to escape. Musashi runs to the home of the Roofworlders, who hide out from the trouble on the streets. Thanks to Musashi's arrival, they are now all in danger, but they manage to fight off the Yakuza's visit with relative ease. The next visit doesn't go so well, with Kotomi-sensei falling ill and the other Roofworlders. With the help of Musashi, the tide is turned and the Four Elements are all defeated in battle, perhaps killed.
Little is known about Musashi's past and why he became Shinobi. The Art of War shows him training with his sensei in the ways of bushido, where he becomes skilled in sword-work, archery and survival. Some prior to his stories in STC, his sensei was killed by the Neo Zeed and girlfriend Naoko was kidnapped. Driven by intense determination, Musashi spent all of his time trying to retrieve her from the corporation. Despite what they would attempt to stop him from reaching his goal, Musashi swore never to kill his opponents, as that would make him as bad as them.
Musashi is highly skilled with his sword, one that can pierce stone, but he very rarely uses the sharp end, preferring to bludgeon people with the hilt. As a 'ninja', Joe can utilise techniques like haragei and prana to gain an advantage over his opponents. He is also seen to be highly intelligent, coming up with strategies to defeat even the most talented of enemies.
Even less is known about the Neo Zeed organisation, although they appear to be corrupt and believe themselves to be below nobody. Their dirty tactics involved poisoning Musashi's sensei and stealing Naoko from Musashi. Although the highest echelons of the company are unknown, The Void was a highly-skilled ninja who was eventually rendered crippled by Musashi. Before this, The Void commanded The Four Elements (Water, Fire, Air and Earth) to do his bidding. Water took the place of Naoko in an elaborate trap to lure Musashi to their building. They were all later seen to support The Void, but later left to join the Yakuza when The Void was defeated. All were highly skilled in ninjitsu and magic abilities, but were defeated by exploiting their weaknesses (such as Water coming into contact with Fire).
It has been said that Neo Zeed have gone beyond simple ninjitsu and gone into the field of magic. Musashi initially branded this as nonsense, but incidents of his haragei being tampered with and powerful attacks from the Elements have cast doubt in his mind.
Naoko is Joe Musashi's girlfriend (or possibly wife) who was captured by the Neo Zeed for no explained reason. She was the daughter of Musashi's sensei.
Roofworlders live on the roofs of Tokyo to evade the crime and prejudice rife on the streets. Led by Kotomi-sensei, the families in the skies were taught valuable survival techniques such as being able to stay hidden and to defend themselves if trouble should come. Sensei trained two important lieutenants, Bunzo and Kinpachi, who helped protect their world when the Yakuza and Four Elements came looking for Musashi. Before this, they were skilled enough to sneak up on Musashi and capture him, evading his haragei, something no normal man could have done.
Musashi's sensei's sensei
In one of many flashbacks, Musashi's sensei told a story to his students about how his sensei became involved in bushido. Originally just a peasant, he stole a sword and travelled to a school to be taught in the warrior way. A guard at the door attempted to kill the poor boy for blaspheming, but the child was strong enough to beat him. Impressed by the skill and desire, the sensei of that school took on the child and taught him survival moves, such as the "chicken-step", that involves running from an opponent, then attacking before the chaser has time to defend themselves.