Prototype
Final
The prototype features a purple sky, for the final it was changed to blue. The floor hazards are also different between versions, and there are no "!" warnings in the proto. The proto is also lacking any items.


Prototype
Final
The kites the ninjas jump out of are missing in the proto, and the ninjas themselves are once again in black rather than green. This stage also goes on for far longer in the prototype, but is missing the golden ninja sub-boss featured in the final.


Prototype
Final
Inside the base, the flashing lights in the background are red and yellow in the proto, but just yellow in the final.


Prototype
Final
The enemies have different colors in the prototype, and the background is also different. Early on in the stage, an item box was added for the final version. It contains a small life item.


Prototype
Final
The hidden area in this stage contains two item boxes. In the final, the one on the right -which contains a bomb -was removed.


Prototype
Final
Right at the top of the stage, there is a platform with two item boxes. In the prototype, one of these boxes has an extra life inside it. For the final, this was changed to a shuriken item.


Prototype
Final
In the prototype, some of the platforms have item boxes with bombs in them. If the bombs explode, they will destroy the platforms. This was changed for the final, so the bombs were removed and replaced with other items (usually shurikens) and the ability to destroy the platforms was taken out.


Prototype
Final
At this point in the proto, there is an item box on the ground which contains a small shuriken item. It was removed for the final. On the platform above, the item box to the left has a bomb inside it in the proto. For the final, it was moved to the right, and contains a large shuriken item.


Prototype
Final
Another item box change -in the proto, it contains a bomb, whilst in the final, it contains a small shuriken item. You can also see that the boomerang enemies have slightly different sprites between versions.


Prototype
Final
At the start of the elevator stage, in the proto you need to move onto the elevator to start it. This was changed for the final so you start on the elevator already.


Prototype
Final
Some of the soldier enemies have different colors in the proto. This opening section also goes on for longer in the prototype, with more enemies to kill.


Prototype
Final
Some of the background details feature very different colors between versions.


Prototype
Final
This part is reversed between versions -in the proto, you come across the two small platforms, then the small and larger platforms. In the final it is the other way around.


Prototype
Final
More item changes (the item in the top right corner was removed from the American and European versions of the game).


Prototype
Final
An item box here, containing a small shuriken item in the proto, was removed from the final.


Prototype
Final
There is a box containing a ninjitsu item here in the proto, in a difficult to reach location. It was removed from the final.


Prototype
Final

Near the end of the elevator ride, the prototype has a platform with a soldier on it, both of which were removed from the final. When the elevator stops in the proto, the next stage starts automatically, whilst in the final, you have to move to the right first.


Prototype
Final

Near the end of the elevator ride, the prototype has a platform with a soldier on it, both of which were removed from the final. When the elevator stops in the proto, the next stage starts automatically, whilst in the final, you have to move to the right first.


Prototype
Final

In the proto, the room doesn't change colors during the boss fight, and the boss doesn't leave a motion trail when it moves. For the final the room constantly flashes red, and the boss leaves a motion trail.


Prototype
Final

The boss has a less explosive death in the proto compared to the final.