Prototype
Final
The map screen has a different icon in the proto. It seems that this prototype is still using the original version's map screen, as you'll see in later levels. In the original version of the game, the first level was going to take place at night, outside and inside a cave. As well as the icon being different, the map itself has several differences, such as there being a mountain at the left, some boats in the sea and the clouds being ever so slightly changed. The font for the round names is also different, as is Joe's sprite and the rock he is standing on.


Prototype
Final
The prototype version features duller colors for the trees and sky. All of the ninjas are black, whilst in final they are green. The prototype also features a slightly different background (look at the grass).


Prototype
Final
The female enemies exclusive to this round wear black in the prototype, but were given brighter colors for the final.


Prototype
Final
In the prototype, the Neo Zeed took the time to neatly stack some of their boxes, but by the final, they just don't care any more. But perhaps more importantly is the fact that in the proto, you cannot break open boxes with shuriken -most of the time, the shurikens will just sail over. This was changed for the final.


Prototype
Final
When you reach the cave, the prototype's background won't change at all, whilst it does for the final. The samurai enemies also have slightly different colors.


Prototype
Final
Just before the second samurai, there is an item box on a platform in the prototype. For the final, it was moved to the ground. The contents of the item box is also different between versions.


Prototype
Final
The sub-boss has slightly different colors in the proto.


Prototype
Final
Inside the cave, the prototype has brighter colors than the final. All of the ninja enemies are still in black also.


Prototype
Final
At the first rope line, there is an item box. It contains a small life item in the prototype, and a full life item in the final.


Prototype
Final
Both of the secret areas in the cave are small in the prototype, but were made larger for the final. This was to fix a glitch that the proto had.


Prototype
Final
The prototype does not feature any of the "Go" signs which are in the final.


Prototype
Final
The parts with the spikes are different between versions. In the prototype, there are some bottomless pits around them, but for the final they were replaced with solid ground.


Prototype
Final
At this point, there is an item box in the proto (it contains a power-up) which was removed from the final and replaced with spikes.


Prototype
Final
There is a part where you need to wall jump up, then drop down. When you jump up, the ceiling is a lot higher up in the proto, and the edges are also different when compared to the final.


Prototype
Final
At this part, there are two enemies in the proto, but for the final, the one in the water was removed.


Prototype
Final
One of the item boxes near the end contains a shuriken item in the proto. For the final, it was changed to a bomb.


Prototype
Final
Near the end of the stage, there is a full life item in the proto. In the final, it is only a small life item.


Prototype
Final
The boss in the proto is mostly the same as in the final, but he has a different starting position and also doesn't move for a few seconds into the fight. He is, however, far stronger in the prototype, taking many more hits to kill. He also doesn't change colors after taking damage like he does in the final.


Prototype
Final
The boss has a different death sequence in the prototype, with small flames appearing all over his body until he explodes. In the final, he has a much more spectacular death, with lots of explosions happening all over him.


Prototype
Final
All of the round clear arts are glitched in the prototype, but work in the final.