Im about to give this another crack just for shits.  I wanna use this thread to devise some sort of strategy that can be employed to beat this game on a semi-regulary basis instead of about the 9 people in the world who have.  (Seriously theres NOTHING online about this game).

First my maps.  Out of the GOODNESS of my heart, I made a map of every level of the game, with the power ups and hazards and yada yada.  Ill be using my maps as a basis for strategy. 

Level 1:
This one is really just a no brainer.  Just for you to get used to the controls.  Nothing to say here, i just always go to the room on the left.  You get a life when you beat the level.

Level 2:
This is where the game all of a sudden ramps up in difficulty out of nowhere.  My strat:

I first grab the green 0 and work on this room.  I ALWAYS seem to have trouble here where I can never clear it quickly.  After some time I go left to room 2. 

In room 2 i use the green 0 in the top right of the level near the green 1.  I then can clear this room out easily.  I go left again to room 3.

In room 3 i use the green 1 ON TOP of the thing shooting out the virus.  This makes clearing the room a breeze.  I then move to the right to room 4.

In room 4 i grab the blue 1.  Theres ONE little square that it seems to be IMPOSSIBLE to clear.  Its whats pumping out the virus.  I think you MUST drop the blue 1 on TOP of this square.  If you miss you might as well restart the whole level.  This room then becomes little trouble with just some patience.  I finally move to the right, to room 5.

In room 5, i cant get a consistant strat.  First i move THRU the virus to grab the blue 1.  I then move back to the thing pumping out the virus.  The same idea from room 4 holds true here, if you miss this you might as well start over.  I use the blue 1 ON TOP of the thing shooting out the virus. This doesnt really make the room easier, just now you have a consistant safe spot.  This room seems to be really challenging and tedious, which is a forshadowing of whats to come.

LEVEL 3: 
This is something i did yesterday that I thought worked well, but i just played crappy.

In room 1, i immediately go right for the super gun (red 0) and blast the hell out of that area and hide in there, dodging the CVs.  After a long time once this room is cleared out I go right to room 3.

In room 3 i run thru it just to grab the blue 1 and go left to room 2.  You'll lose your super gun.

In room 2 i use the blue 1 on the virus thingy on the top right of the screen.  Then go back to room 3.

In room 3, with the super gun this room is relatively easy.  After this ill move left to room 2.

In room 2 you'll have your CCV active to take care of a lot of virus.  Use the SG and clear this room out.  You dont
really need to take care of the virus thingy on the bottom left.  After this i grabbed the blue 0 and moved to room 4.

In room 4 I used the blue 0 ON TOP of the middle virus.  This doesnt work THAT well but if you can prevent the virus
from really going haywire in this room you'll be ok and with some luck can wipe this area out quick.   Then I use the bottom left exit and go to room 5.

In room 5 you can clear the virus out mostly with the SG which isnt too bad, just time consuming.  After this grab the green 0 power up go right to room 6.

Room 6 isn't too bad, but you can get tripped up by the SSV. THATS the hardest and trickiest part.  If you die in this room you have another super gun.  If you die again its still beatable (when you die you appear on the bottom right of the level) just takes caution and patience.  Throw your green 0 somewhere in here and get back your SG and clear this out.  The trickiest part is towards the bottom right of the room.  If you die you start there and lose your SG.  Good news is since you die you'll have a sheild and can kinda work around in there.  AND theres an extra SG gun in this room.

LEVEL 4:  Trying this one.
Room 1, grab the SG and just go to town in this room.  This one isn't too bad till you get to the virus in the middle.  Then exit bottom right to room 5.

In room 5, this room is really easy until you get to the middle where the SSV is being a pain in the ass in the middle.  Theres a way to glitch it so they dont shoot SSVs but i dunno how.  After this room is clear, grab the blue 0, and move bottom left.

In room 4 I throw this down over the virus on the left.  Be careful because the proxy SSV on the bottom right will only shoot if you're close to it and spread more virus.  Do it quick and bounce and keep moving right to room 6.

In room 6 this is a piece of cake room.  Grab the green 1 and put it over the virus and clear this sucker out.


LEVEL 5:
No consistant strat.

Tips:
If you're about to die and you have the super gun (red 0 or red 1) try to go somewhere to replace it with another power up.  If you die, you lose your super gun (unless its purple 1 which is only found in level 5).  Your other power ups will stay with you when you die.  The super gun is practically essencial for level 4 and 5.  Level 3 can be beaten without it, but it takes a VERY long time.

I heard this game was hard... Don't have it yet but I'm definitely gonna use those tips if I ever get the chance to play it.
Is it really as bad as people say it is?

This game is mind-numbingly frustrating. Can confirm. Thanks for the strats. I'll give them a shot.

Also for what its worth, the code from gamefaqs (Up + A + B + Select then start at the title screen) seems to be a level warp to level 3. So you can skip the first two levels.

I don't like saying it's hard.  Like I don't like saying driving a salom corse on ice is hard.  It's not easy for sure, it's just, tricky.  Think of playing pac-man, with a gun, and controlls like astroids.

Of course, that wouldn't be allowed for the competition thread.

hah for this game it should be! Those 2 shouldn't even be called levels but 'demo levels'!

I just tweaked level 3 a bit after i just played it and seemed to work decently.

bumped because i added a little to level 4

bump

Can you explain the countermeasures a little bit? What are SSVs?

Its in the manual. The Counter Measures are the things you get to help you, whether its the super gun, or a capsule that shoots out antibodies in a specific direction (Green 0s go up and down, green 1s go left and right).

SSVs are the computer systems 'white blood cells' that'll kill you in one shot. Also towards the end, some only shoot out when you're close and will add more virus to the room.

well, if you have to like write out a game for it, than its surely hard

Im bumping this because I actually played it 2 nights ago with the same strategy as above and got just as far to level 4. My run also stopped at level 4 because I didnt have a strategy for the rest of it. Lets get this going again, for some of the more hardcore NES'ers out there.

If you wanna help come up with a strat, either try on an emulator, or on a real NES, if you hold UP + A + B + Select then start on the title screen, itll bring you to level 3 and you can work from there.

I really want to give this game a try. Nice strategy guide.

If you find anything new, let me know! Ive wanted to work on this, but no one wants to help me get a workable strategy for level 4 and 5. If I end up doing it by myself, I wont be sharing it  

I really don't want to play this again, but I will give it a spin in November to try to map level 5.
I did it under heavy influence of booze the last time.

I mean, anyone can beat it, its just how long do you want to keep torturing yourself ya know? How many hours do you want to play the same level over and over again?

Id like to get something down where it can be beaten every time with minimal effort. So a strat that effectively uses the components given in the best rooms with the most efficient method. Im happy with what I have so far and worked for me when I replayed it a few months ago. I still firmly believe its a puzzle game.

It definitely is a puzzle game.
It felt that deploying certain items at certain places sped things up a lot when I was playing it.

Hehe, I gave in to the temptation and ordered it. But considering I live in Europe and I ordered it from the US it will probably takes ages to get(or so it tends to). But yes, I will share whatever I find out, if I get anywhere at all! 

I got my cart from the US today, guitarzombie! Lets see if I can help out with your strategy guide. Can't promise, but I will try. 
After reading everything ever written about this game on NintendoAge I'm really curious what this weird weird game is all about.

If you ever get something of a complete theory would you consider making a strategy guide for GameFAQ? 

No way  .  If we do all the work, WE should reap the 'benefits', whatever that is haha.  Their gamefaqs strat is garbage.

Oh the fruits we'll bear! 

Okay, okay. Well. I know NA user Elkovsky, who managed to beat Q*Bert, which is also quite the acheivement, was encouraged to write a strategy guide, by Staryice and Crabmaster2000, I believe. I've struggled with Q*Bert. His guide has been really helpful, although I am still not near mastering the game. I thought it could be a cool thing if something like it was made for Mutant Virus, if a complete theory was ever to be made, but thats definitely up to you, guitarzombie. The work you've done so far is good. 

My first impressions of the game:
Only been playing a couple of rounds now. I have been trying to avoid watching videos or reading too much of the gameplay, to keep a pure first impression.. and wow, its definitely a different type of game. What nobody told me, and what caught me by surprise is these Ninja Gaiden-esque storylines between the levels with our hero being sent into the machine, and an actually story unfolding between the gameplay. Pretty neat. Our hero looks a bit strange, but its still cool they did this. So far I like the game. 

Playing level 1 was like, "Hey this isn't that bad, I can do this." Just spraying this stuff on the virus and neutraulizing the area around the black viruses, and suddenly the spread was destroyed. I couldn't figure out 100% why sometimes my shooting rampages were effective and sometimes they seemed to have little to no effect, but to a degree it made sense, and in the end I did clear the first rooms. Shooting the walls around the viruses seemed to be a good strategy. It sort of made a frame around the spread, and it became easier to kill the rest afterwards. So I just do this in three of the rooms, and great. Level 1 done. 

Level 2 however the viruses seemed far more aggressive, and I couldn't get it under control as I succeeded doing in level 1. Instead I had to back off. Overwhelmed by the intensity of the viruses. Leaving the first room and coming back was not a good idea either, because while coming back the whole room was infected. Yikes.. 

I found some kind of item with the number 0 and 1, and I haven't been able to understand what they do. Right before turning the console off for today I understood that by the SELECT button one have different types of weapons. I counted 4, but after using the one called "CM" it disappeared. It didn't seem to shoot, unlike the others. The other weapons seemed to indicate 3 different ranged-style of the weapons, perhaps strength too? I expect there is strategies with these weapons to handle the virus spreads. I'll have to experiment with this. 

Thats basically my progress so far, which obviously isn't much so far, but just to note some first impressions to this weird but fascinating game. Intrigued that this may be a puzzle game in disguise. It might be right. I'll keep that in my mind, and when I feel stuck enough I'll try to use the guide. 

In my maps i have the locations of the little power ups and what they do. I forgot off hand but they do different things. Some deploy straight up and down, others left and right. Others left on an angle, right on an angle, a super gun and a mega super gun you dont lose when you get killed.

My whole point is knowing which rooms to tackle first with what of those power ups to deploy in the best room in the right spot. Ya dig?

Go thru my guide.

Yes, that makes sense... Your guide will no doubt speed up my 'progress'. Thanks. I just wanted to try it out without a guide first.

What for example is like the best way of handling the first room on level 2? It seems like sometimes the viruses are easy to kill but sometimes it is difficult for any progress to be had. I suspect a lot of people who play Mutant Virus just shoots until something eventually works? I realize the power ups will help, but I wish I understood what I'm doing, and what I'm looking at. There must be some kind of system to the madness? 

I think I read somewhere that if there's like 9 viruses in a lump together, and 5 of them are in the pink field and 4 are in the turquoise, the 5 in next step takes over the 4, because 5 is more than 4.. and so on. Is this true?  

These are the rules for John Conway's game of life, which the Mutant Virus appears to follow to some extent:
For a space that is 'populated':
Each cell with one or no neighbors dies, as if by solitude.
Each cell with four or more neighbors dies, as if by overpopulation.
Each cell with two or three neighbors survives.

For a space that is 'empty' or 'unpopulated'
Each cell with three neighbors becomes populated.