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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.

AlchemyEdit

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:

A B C D E Recipes
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
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
- - - - 500
- - 100 - - Cicada Shell
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

Cicada Shell
- 24 24 - -|
Any three compounds with a value of 7. For example: Canine's Sense
7 7 7 - -
1 3 5 7 - Double Jump
2 4 6 8 - Double Jump
8 9 8 9 - Ninja Flame (Red)
- 8 9 8 9 Ninja Flame (Red)
All compounds should be 33. For example: Ninja Flame (Black)
33 33 33 33 33
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

Invisible Shadow
- 44 44 - -
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

Master's Understanding
- - - 55 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
99 99 99 99 99
Any compound with a value of 333. For example: Limitless Weapons
- 333 - - -
Recipe: Add 100 Special Mushrooms to an empty pot.This item can be re-extracted anytime. Alchemical Genius Mix +999
999 999 999 999 999
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

Special Mushroom
- 3 3 3 -
Any 2 compounds with a value of 11. For example: Special Mushroom
- 11 11 - -
Any 2 compounds with a value of 10. For example: Evenweed
- - - 10 10
4 6 4 9 - Salmon
- - - - 24 Camouflaged Land Mine
- - - - 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
- 4 - - 14
Two compound values that summed make a total of 28. For example: Camouflaged Strong Land Mine
4 - - - 24

Shinobido 2: Revenge of Zen Alchemy Edit

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.