The game's story begins in the year 1256, Kencho Era Japan, where the young Oboro Clan Leader Jiro Musashi (father of Joe Musashi, the main character from the original Arcade and Sega Genesis Shinobi games) is summoned to defend his home village from the ninja forces of Zeed.

As he battles on, he begins to uncover a deeper conspiracy (depending on the level of skill and difficulty), a secret mission is unlocked, revealing an ancient alien Orn that instigated the events in the Kamakura era, including the betrayal of Jiro's own teacher, in hopes of creating the most powerful Ninja army in space.

[6] Destructoid praised Shinobi 3D for having "tons" of content, but noted that the steep difficulty curve and lack of coherent narrative may turn off some players.

[7] Official Nintendo Magazine UK similarly stated that "Shinobi won't be to everyone's tastes since we're now in an age where games are expected to be easy enough for everyone", but said it should be enjoyed by players looking for a challenge.

[9] However, GamesTM was more critical of Shinobi 3D, judging the "unsympathetic difficulty" of the game as "cheap and archaic within the context of plodding action".