Advancing through the story will eventually unlock the Alchemy option, which allows the player to create their own tools for missions. These tools are created by mixing herbs, mushrooms and geckos in medicine jars and then collect the mixture in spheres, medicine bottles or sushi for later use. Scrolls and permanent stat-increasing medicines can be created this way too.
While one alchemy pot is available as soon as alchemy is unlocked, more can be bought later. Ingredients can be bought, but for the rarer ones you will need to find them during missions.
It's recommended to take Collection or Reccoinassance missions if the player wants to gather ingredients quickly. Study the maps carefully, as many areas have "special spots" that may spawn rare or large numbers of ingredients.
Some stray arrow messages contain hints for some recipes and their effects.
There's no need to bake items for these combinations to work, just drop them into the pot until you get the desired result.
Note: When making potions and spheres, positive values have positive effects and negative values have destructive effects, so use positive values to make potions and use negative values to make spheres. Also, if you add a positive value to a negative one, or vice versa, it will take away from the total numerical value.
List of combinations:
|1||2||3||4||-||Health Potion of Heart|
|100||-||-||-||-||Health Potion of Liver|
|-||100||-||-||-||Health Potion of Lung|
|-||10||20||30||40||Health Potion of Kidney|
|???||???||???||???||???||Spleen Medicine of Health|
|4||3||2||1||-||Strength Potion A|
|-||-||-||100||-||Strength Potion B|
|-||-||-||-||100||Strength Potion D|
|Any compound with a value of 500. For example:||Strength Potion E|
|Any two compounds with a value of 24. For example:
Recipe: Drop 2 Special Mushrooms in a pot, then add 2 Gambler Mushrooms, and finally 1 Evenweed
|Any three compounds with a value of 7. For example:||Canine's Sense|
|8||9||8||9||-||Ninja Flame (Red)|
|-||8||9||8||9||Ninja Flame (Red)|
|All compounds should be 33. For example:||Ninja Flame (Black)|
|Any two compounds with a value of 44. For example:
Recipe: Drop 4 Special Mushrooms in a pot, then add 2 Gambler Mushrooms, and finally 1 Evenweed
|Any two compounds with a value of 55. For example:
Recipe: Drop 5 Special Mushrooms in a pot, then add 2 Gambler Mushrooms, and then an Evenweed to make all values 54, use other ingredients to make 2 compounds with a value of 55
|Recipe: Drop 10 Special Mushrooms in a pot, use other ingredients to make 1 compound value between 495~499, then add an Evenweed||Limitless Weapons|
|Any compound with a value of 333. For example:||Limitless Weapons|
|Recipe: Add 100 Special Mushrooms to an empty pot.This item can be re-extracted anytime.||Alchemical Genius Mix +999|
|3 lined-up compounds with a value of 3. For example:
Recipe: Use your ingredients to make 1 compound value between 15~19, then add an Evenweed
|Any 2 compounds with a value of 11. For example:||Special Mushroom|
|Any 2 compounds with a value of 10. For example:||Evenweed|
|-||-||-||-||24||Camouflaged Land Mine|
|4||4||4||4||34||Invisible Land Mine|
|45||-||-||-||-||Strong Land Mine|
|One of the compounds should have a value of 4, and E should have a value of 14. For example:||Strong Land Mine|
|Two compound values that summed make a total of 28. For example:||Camouflaged Strong Land Mine|
1. Alchemy Basics (Credit: Serenitychan 2007)
Alchemy is located in Equipment section. You need to have it activated first after a certain point in the story. Just do the story missions and you'll get it. I don't recommend doing alchemy til you have a good share of Money or herbs/mushrooms. Basically you use those ingredients to create items. And then you use those created items to make other items. It's a skill you need to learn to get 100% out of this game. If you don't know Alchemy and all the wonderful things you can do with it, you are missing out.
You won't be able to do without alchemy:
- Play Very Hard
- Robbery missions (contract: kill none or be “invisible”)
- [Reasons why you should use +999 items]
Whether or not it would make the game too easy is ridiculous, in Very Hard difficulty, Kabuto is insanely hard. So if mashing the same 1 on 1 combat buttons for 20 minutes is your idea of fun, all the while trying to avoid his shocking damage, be my guest, but as for me, I'd rather pump a couple of +999 grenade spheres into him and get it over in 2 seconds.
This game is about Stealth Kills. Where SK's fail, items reign.
It'll be fun for a bit to use them a lot, then you will just use them in hard missions (with difficult bosses) in very hard mode. There is, after all, no fun in a non-challenging game. I agree with that 5 Words.
Robbery Missions: Don't kill anyone. +999 Unconscious sphere, anyone?? These are impossible to do without +999 Unconscious spheres, without levelling the whole stage, which breaks the contract, which ruins the point of the game to keep contracts. Of course you CAN do without but you'll be constantly using the same hand to hand moves on those bosses and it's just ridiculous, when you can chuck some +999 bombs, and get it over with in 2 seconds, and continue about your Ninja business.
This FAQ will teach you how to make Special Mushrooms, Limitless Weapon scrolls & the all powerful, mighty and hailed Alchemical Genius.
To start alchemy, do the following:
- a. Collect 11 Special Mushrooms
- b. Collect Even Weeds
(They distribute pots TOTAL VALUE among 5 compounds) c. Pick up all items in missions and circle (O) them when you're at home, to put them into your home storage and use later.
If you already are doing C and have A bunch of weeds and mushrooms you can use, then proceed to making special mushrooms.
2. Special Mushrooms [Beginner Level] 
Might be the best item in the entire game. Of course it *isn't* but it certainly helps you get the best items in the game.
What they do in Alchemy, is add a value of 10 to the highest value. What's beautiful about them, is if there are two or more values which are the highest, all of them get an added value of 10. That includes all zeros, a clean pot. Which means 0, 0, 0, 0, 0 becomes 10, 10, 10, 10, 10 when a special mushroom is added ^_^
If you don't already have some from picking them up, follow this easy and simple method to get them. You need as many even weeds as you do special mushrooms. Say you need 5 special mushrooms to get 11, you need 5 Even weeds. Luckily for us, they can be bought in "buy ingredients" shop.
Special Mushrooms are made by the values 3, 3, 3 next to each other.
3, 3, 3 can be in A, B, C or B, C, D or C, D, E.
A, C, D = No.
If you aren't following me so far, go read your shinobido manual xP
How to get 3, 3, 3 easy
- Make your TOTAL VALUE of compounds 15-19
- Add Even Weed
- Extract Special Mushroom
Note: Total Value refers to the pool value of all compounds. For example:
-1, +5, -3, +10, +2 has a TOTAL VALUE of 1+5+3+10+2 = 21
Do this however many times you want, and when you get 11, go to section 3.
3. Limitless Weapons (LW) [Intermediate Level]
Limitless Weapons, are beautiful, beautiful scrolls. They are perishable, but last an entire mission. They allow you to throw/use things infinite times during the entire mission. Think of the possibilities and multiply that by an infinity.
You need a clean pot with 0, 0, 0, 0, 0
- Add 10 Special mushrooms to make 100 x 5 Current Total
Value is 500
- You should have 1 special mushroom left over
- Limitless weapon requires 99 x 5, this is where Even Weed
comes into action.
- Using same method as before, make the TOTAL VALUE add to
495-499 with any ingredient. Check bottom line to see what'll get you 495-499
Example: 99, 101, 98, 100, 99 = 497 = OK
- Use an Even Weed, to make this now 99 x 5
- Extract Limitless Weapons
Now you have a decision to make, do you want easy Money (in game currency) or don't want the game to be too easy? If you want Mon, do the following:
Go into your equip menu and put these things, in your throw/use slots
- a. 1 Limitless Weapons (LW)
- b. 1 Even Weed
- c. 1 Special Mushroom
- d. 1 Valuable Gecko
- e. 1 Salmon
If you don't want to make money, don't worry about putting in the Salmon.
Once a, b, c, d & e are done, Go play in your garden.
- Find a nice corner
- Use Limitless Weapon
- Start throwing your Special Mushrooms out
- After 50 the game is going to get pretty laggy (on my machine it does) so pick them all up and keep throwing more out. Do this til
you accumulate over about 300 of them.
Do this step with Even Weed, Valuable Gecko and Salmon
100 Salmon = 70, 000 Money
When you have several hundred Special Mushrooms, and some more Even Weeds (optional), leave and proceed to making Alchemical Genius (AG)
The Valuable geckos are to add to your AG pots to make them multi compound active ie: you can extract potions which give you +speed + strength + cure all in one.
If you opted to make money, sell your x amount of Salmon that you cloned in garden for lots of Money. If no, you can always make more LW scrolls later with all of those Special Mushrooms and do what you like.
4. Alchemical Genius [Advanced Level] 
These are awesome. These are what allow you to create +999 spheres and potions.
First, this is how you make them:
- Find an empty pot
- Put 100 Special Mushrooms in it, to create 999 x5
- Extract Alchemical Genius
Now go into BUY INGREDIENTS, and if you took the Salmon with you before, the money is really going to help here.
Buy as many Empty Spheres/Bottles as you can afford, or however many you want.
Now go back into alchemy and you have a decision to make.
You can choose between the following +999 items, all potions are positive of the compound, and all spheres are the negative of compounds.
(Note that you can make the positive, spheres also [to help allies for example])
A Cure potions? or Confusion spheres?
B Strength potions? or Weakening spheres?
C Speed potions? or Unconscious spheres?
D Potency potions? or Amnesia spheres?
E Health Potions? or Explosive spheres?
- make one AG full of all positive, and
- make one AG full of all negative.
Because you can make spheres and potions which have multi active stats, dupe some valuable geckos for this. Every Valuable gecko you add to your pot lets you have one additional active stat. If you add 4, you'll be able to have all of AG's ingredients active, however, it just sorts them by highest -> lowest.
So say you added two valuable geckos and your AG pot has the following
values: +999, +990, +991, +992, +995
The active values will become +cure +potency +health. And you can make your sphere/potions with those 3 active stats. Note it won't say it in the description, but when you use it in mission you'll gain health, while getting immunity and potency stat ups for a limited time.
You should also get +1 in both flavours (green and yellow) geckos, for every single compound. This is because you can actually manipulate the pots active compounds themselves with the geckos, Regular +1 geckos can be found in "BUY INGREDIENTS" and cost 600 Money each. I think it'd be good to take all 10 Geckos with you and LW scroll them in your garden to get at least 50 of each, as well as some valuable geckos. That will last you pretty much forever.
For an easier time using alchemical genius to get all + or all -, try the following:
- Look if any of your pots have the correct flavours you need on all compounds.
- See if any ingredients you own have the right flavour set to change your pots flavours (or try the shop).
- When all else fails, put in the AG, take out the AG, for a new random AG compound flavour set.
When you decide, put your Alchemical Genius into a pot which will produce the values you want. (-A +B -C , etc) The pots are different so each one will produce something different. Just decide what potion you want for now. The Alchemical Genius won't be wasted, I'll tell you why in a bit.
So say you wanted to make Explosive Spheres and Unconscious Spheres. Then you can have X, X, -C, X -E where the X's you don't really care about.
So as long as the pot gives you the spheres you want, then put the AG into it. When you do it you'll notice it'll say either CURE/CONFUSION.
That's because of DOMINANT VALUE.
[Now learn about DOMINANT VALUE]
A dominant value is the value which is highest in the pot. It shows by writing underneath the compound. When values are all the same, A, or the one closest to A, gets priority.
Using this knowledge, we can manipulate the 999 x 5 (CURE/CONFUSION) very easily. Go into Buy Ingredients and buy a bunch of Geckos (both yellow and green flavour) that +1 to A, B, C, D. They are found at the bottom of the ingredients list.
Manipulate the DOMINANT VALUE by +1 with a gecko to make it either +998 or -998. Then the next dominant value is now STRENGTH or WEAKENING.
Do it with compound B now, and you can now make your unconscious spheres (assuming you want them).
Simply put in EMPTY SPHERE into the jar, and it will produce an item the name of the jar with it's value next to it. Ie: You named the Jar "Knock Out" it will make Knock Outs +999
Note: Renaming your jar before making item helps you to remember what the item is that you are using. They are colour coded, though.
[Now learn about AMOUNT REMAINING]
1. When you extract potion/sphere/sushi you -1 Amount Remaining.
2. Every time you put in an AG, the pot gets +99 Amount Remaining.
3. Abuse this by getting to 3-4 Amount Remaining, then doing the following:
4. Add Even Weed to pot making A, B, C, D, E values all the same
5. Special Mushroom pot back to 999 x 5
6. Extract Alchemical Genius
7. Put Alchemical Genius back into pot (or different one if you want new spheres/potions)
You can do multiple items from the one Alchemical Genius.
You have infinite "amount remaining", so long as you have Special Mushrooms and Even Weeds, and as long as you have EMPTY spheres/bottles/sushi, you have infinite spheres/bottles/sushi with the effects you desire.
You can now manipulate and make items however you wish.
For a full understanding of neat tricks to do in alchemy, I recommend that you read the entire section 5. (especially about multi status)
5. Some Alchemical Genius Tricks & Tips 
[How +999 Effects all items]
Value Relates to Time that the User is under effect -
- - Cure
- - Confuse
- - Strengthen
- - Weaken
- - Speed
- - Knockout
- - Potency
- - Amnesia
Value Relates to power of the item
- - Heal
- - Explosive
Adding Valuable Geckos to your AG pot is quite ..valuable
The more you add, the more compounds will become "active".
You can extract items with multiple active abilities this way.
So you can have a health, speed, strength, immunity, potency potion, all in one XD (likewise for negative spheres).
[Getting the first 100 items that you want, trick]
Here's an easy way to manipulate your "AG POTS", the very first time you make one from the special mushrooms.
Find a clean pot, and do the following. If you want a compound to be +/- , have some +1 geckos, both flavours, for all compounds ready.
If its a Yellow 0, for +1 you'll need to add a yellow gecko.
For -1 you'll need to add a green gecko.
If it's a Green 0, you need a green gecko for +1, and yellow for -1.
If the gecko you need is unavailable, try a correctly flavoured swap weed.
When you extract the Alchemical Genius (after your amount remaining has dwindled down close to zero), the +/- and flavour seems to be completely random.. :o Then you have to re-do this trick to a pot, but instead make it so the pot flavours will fit with your AG to make the AG pot how you like. You can't use geckos again though, unless the ONE gecko has the flavour set that you need =( Try to collect various flavour sets in forms of geckos/even weeds/swap weeds/valuable geckos, etc. XD
[Speed Potion +999 trick]
Do this for "duping" in the future.. take your LW scroll, and whatever you want to duplicate, and a speed potion +999.
Use LW scroll, then speed potion. You will now throw AND pickup about 2-3x faster than normal.
Edit your garden a 1 square deep pit to jump into for cloning items. Easy throwing, easy pick ups.
Any type of sushi you want, such as knockout, etc.. can be cloned.. just do one of each type you want (name them differently) and take them with you to be cloned
[Something smells fishy]
Another trick is duplicating your Salmon! Each one sells for 700Mon, use it to buy all things from the shop rather than cloning things from the shop.
It's the most economical way, anyway.
As a side note, Salmon can also distract bears, so that you are able to stealth kill them once they've begun eating it!!
Shinobido 2: Revenge of Zen Alchemy
Alchemy remains mostly the same as before, with two new features:
- "Super" tools can be created via alchemy. These "super" items have stronger effects than their common counterparts.
- The Network Jar, which lets players use wireless connection to add an ingredient to a shared jar and extract multiple items at once from it.