I've been wondering about this for a long time, and after a google search, this seemed like a good place to ask. I'm trying to track down an arcade game from my youth; it was definitely an arcade cabinet and not a console game, though I've never seen it anywhere other than my old hometown arcade (now long gone, sadly, so I can't ring them up and ask). However, I grew up in a pretty small town, so I can't imagine we got anything *really* obscure.
The game was set in historical Japan. I can't remember if you played a ninja or a samurai, but it must have been one of those. It was a top-down, vertically-scrolling game, mechanically somewhat like Ikari Warriors, though I feel like the sprites were somewhat smaller than in that one. I don't think it used the rotating joystick either, but I'm unsure about that.
I never got much beyond the first stage, which was in a city street. You moved forward, killing baddies as they came, and occasionally there was a door in the side of a building you could enter. These went into rooms where you could fight some extra bad guys in exchange for a new weapon (I think I remember nunchucks specifically) and then return to the street where you left off. I *think* when you got to the end of the street, there was a boss of some sort blocking the gate to the next area, but when I try to picture it, all I can remember is a similar scene from Golden Axe, so that's not much help.
I always got killed pretty quick in the second stage, but I remember it as having bridges over canals, and yellow-suited ninjas that jumped out of the water and threw sais at you -- diagonally, in pairs. The ninjas may have jumped out of pots as well, maybe? But I definitely remember pairs of sai criss-crossing the screen in diagonal paths.
Anyone have any suggestions or clues? This has been bugging me for *ages*.

