A prototype version of Shadow Dancer was released by drx of The Hidden Palace on the 2nd of May 2016. It's a late build of the game, with a build date of October 2nd, 1990, but it still has quite a few minor differences when compared to the final:

Prototype	Final
After the SEGA logo vanishes, the prototype has just the word "SHINOBI" at the next screen. The final has "THE SECRET OF SHINOBI".

Prototype	Final
The prototype's copyright is 1991, and the game's title has no trademark. For the final the copyright year was changed to 1990, the word Dancer was moved a little to the left and a TM was added.

Prototype	Final
The intro text is different in the prototype, and features quite a bit of Engrish. It also doesn't mention Neo Zeed like it does in the final, and perhaps the biggest difference is that it specifically calls the main character "Hayate". In the final version, the name Hayate isn't there, instead, the character is just called "Shinobi". The instruction manual for the Japanese version reveals you're playing as Hayate Musashi, whilst the American and European manuals state you are playing as Joe Musashi, the ninja featured in the original Shinobi arcade game and the Genesis sequel, The Revenge of Shinobi. Meanwhile Hayate is Joe's son.

Prototype	Final
At the main menu, the prototype has just "OPTION", it was changed to "OPTIONS" for the final version. The text and arrow were also moved very slightly higher.

Prototype	Final
In the options menu, the difficulty level settings are referred to as acts in the prototype, for the final, they were changed to levels. The BGM test is missing several pieces of music in the prototype, despite the music being in the game. You can only listen to 10 different tracks, whilst the final has 19. Also, you can't stop the music in the prototype -in the final, pressing the B button will stop the music. The SE test is also missing a few entries. There are 43 sound effects, whilst the final version has 46. SE 09 doesn't work in the prototype, it plays nothing when selected. Instead, what it SE 09 in the final is SE 10 in the prototype, meaning the proto's SE test lags behind the final by one. Two of the sound effects is also different -the noise made for when the enemy soldiers fire a bullet sounds like this in the prototype, and like this in the final. The sound effect for causing damage to most bosses is also different -it sounds like this in the prototype and like this in the final. The voice effects Joe and the dog have can't be heard in the prototype's SE test, but were added in for the final. Even though the prototype main menu just has "OPTION", it still reads "OPTIONS" at the top of the options menu, like in the final.

Prototype	Final
The round title cards feature an odd choice of colors in the prototype, but maybe they're glitched. They were fixed up for the final version.

Prototype	Final
The above difference also effects the stage start screens.

Prototype	Final
The prototype is missing the "EXIT" signs that pop up at the end of a stage, these signs are present in the final.

Prototype	Final
This one is difficult to show or prove with images, but during the two tremor sequence in the second stage of round one, you can't move left or right in the prototype. You have to wait for the screen to stop shaking, which seems to go on for a little longer than in the final. You can use a magic attack and jump though. For the final, this was changed so you can also move around and throw shuriken. Whilst I'm here, note that the 1P in the top left corner is further away from the score in the proto than it is in the final.

Prototype	Final
The lightning bolt that reveals the boss is yellow in the prototype, but was changed to blue for the final. This applies to all boss fights in the game. Also note that during boss fights, the prototype still has the word "SAVE" in the bottom right corner, despite there being no hostages to rescue in boss stages. This text was removed for the final version.

Prototype	Final
The head of the first boss will not flash in the prototype for when he's standing still, but it does in the final version.

Prototype	Final
When you defeat a boss in the prototype, you will bounce off them if you try and walk or jump into them. This doesn't happen in the final version.

Prototype	Final
The Shinobi bonus -rewarded for beating a stage without using any shurikens -is only worth 10,000 points in the prototype. This was upped to 50,000 points for the final version.

Prototype	Final
In the prototype, the bonus stage starts immediately. For the final, they changed it so the text flashes a bit first, and then Joe/Hayate will jump down. And yeah, the colors for the text are still different, with the same odd colors seen earlier.

Prototype	Final
Hitting nothing in the bonus stage results you getting 1000 points in the prototype. Doing the same thing in the final will give you an extra life. Joe/Hayate lands slightly higher up in the final than he does in the proto.

Prototype	Final
The bonus stages are much easier in the prototype as the enemy ninjas move at a slightly slower speed, plus there are less of them -only 46, compared to the final's 50. However the prototype lacks the "PERFECT" message for getting them all that the final has.

Prototype	Final
The round two boss is easier to beat in the prototype, as he'll only attack you with one arm, whilst he has two in the final. However, it seems like in the prototype his single arm has a longer reach.

Prototype	Final
The round 3 boss head doesn't flash in the prototype, whilst it flashes orange and yellow in the final.

Prototype	Final
This boss is harder in the prototype, because if you touch her smaller spinning blades, you'll die, whilst in the final, you just get knocked back. Another point is that when the boss throws her larder blade out across the ground, it doesn't make a noise in the prototype, whilst in the final, it does. However, this noise isn't in the SE test so perhaps they added it late on and then forgot to add it into the test.

Prototype	Final
The round 4 boss seems to flash red in the proto, and white in the final...unless you play the proto on the act 3 difficulty setting, where it will flash white like in the final.

Prototype	Final
Each room of the final round has a 3 minute time limit in the proto, but the timer was removed from the final version.

Prototype	Final
The room title cards all feature the odd coloring in the proto, but the final boss card features the text in a different layout than what the final version went with.

Prototype	Final
The final boss fight begins straight away in the prototype, for the final, they changed it so everything is dark for a few seconds before the lights come on.

Prototype	Final
The lightning bolt caused by the boss when he summons his minions is yellow in the proto. It was changed to blue for the final.

Prototype	Final
The credits seem to go faster in the prototype than they do in the final. "MAKING STAFF" became just "STAFF", and several of the credit names are different. drx pointed out that in the proto, the staff are using their real names, whilst in the final, they are using aliases.

Prototype	Final
More credit differences.

Prototype	Final
More credit differences. The colors also change earlier in the prototype -making the credits more difficult to actually read.

Prototype	Final
More credit differences.

Prototype	Final
Beating the game on the first difficulty setting results in no to be continued message in the prototype, which was added for the final.

Prototype	Final
The same thing happens on the second difficulty setting.

Prototype	Final
Beating the game on the third difficulty setting results in no message in the prototype, whilst a "THE END" was added for the final version.

A couple of other things about the prototype. Firstly, if you manage to get more than 20 lives, the lives counter will feature glitchy graphics at the stage start screens. This was fixed for the final version. There is also a glitch in the final boss room -if you keep jumping towards the right, you'll be able to get off the screen. You won't die and the boss won't be able to hurt you, but the enemy ninjas can still get to you. You can't get off the screen in the final version.

The music also stops in the prototype for whenever you use a magic attack. It doesn't in the final.

Make sure to check out The Hidden Palace for more prototype rom stuff.