Number of stages: 5
This level seems to be one that never made it into the original version of Shinobi III -I've seen no screenshots of it in any magazines. The boss would, at least, make an appearance in it.

 

To end this first stage quickly, kill the single soldier you see and then just run right. However if you head upwards instead you'll find other enemies, including more soldiers and a few ninjas.

The next stage has you moving upwards, using the girders to do so. Enemies are once again just soldiers and ninjas. Once you move far enough up, the next stage will start.

Stage 3 is another case of just running right a little bit to complete it, although you have the choice of using the top or bottom floor.

The next stage is set outside, and you'll encounter a couple of robots. These robots will shoot many shots at you, but they will do far more damage if they dash into you. Killing them will give you lots of points, but you'll probably have to use a ninjitsu magic to destroy them.

After defeating or avoiding the two robots, drop down and walk along for a bit. There is another robot down here, but you can avoid him just by staying on the girder above. Walk towards the end of this girder and the stage will end.

The boss of this round will then appear. He does make an appearance in the original version, but at a different stage, and it isn't clear if he is a boss or a sub-boss. He also makes an appearance in the final game, but only as a sub-boss. Anyway, in this prototype, just walk past him and the round will end. At the round clear screen, there is artwork of Joe defeating this boss. Note the girders behind him, which aren't present at the boss stage itself.