Overview:
This mod introduces a disease system to Skyrim. Before this, diseases were merely debuffs that you instantly acquired and instantly got rid of. Now diseases progresses slowly and grow stronger or weaker, depending on several factors.

You can learn how to cook home-made medicines (after reading a book on how to do it), craft potions to cure a specific disease (or a poison to cause their effects), get sick eventually when exploring infected places, try a cure by resting or die by leaving a fatal disease unattended...

Diseases effects were carefully loyal to the original ones, but added some side-effects that make it more interesting. For instance, if you are infected with a certain disease that causes your hands to shake, you might have a spasm when overdoing physical activities. Also the regular effects have been reduced drastically on early stages and increased drastically on advanced stages.

1.Progression:
Each disease has 6 stages, being the first one pretty really mild and the last one really powerful. Each disease has a specific time to an “evolution check”. In this evolution check, it is possible that the disease evolves or recedes.

2.Evolution Check:
First test is to check if the disease evolves. If not, a second check is made to know if the disease will recede. Even without Disease Resistance, players always have a chance to resist the disease. The probability of progression or recovery of a disease depends on some factors:
a)The player's Disease Resistance: If you really want some disease immunity or resistance, you need this. The greater this value, the greater the chances the disease will not evolve, or even recede. A 100% Disease Resistance yields a 100% chance to resist and go back one stage of the disease. Anything described below yields a much lower chance to resist the disease.
b)The player Health: the greater the health, the greater the chance to pass both checks.
c)Is the player resting properly? No resting state yields a penalty to the check, while well rested and marriage rested yields a bonus. The location the player is also affects a lot this check. Dirty places like dungeons, cemeteries, caves yields a high penalty, while staying on clean and comfortable places like home, temples, inns or even in cities yields a huge bonus. The cleaner the place, the better!
d)Is the player under effect of medicine, potions or blessings? This leads to the next feature.
e)Disease stage: recovering from a early stage is much easier than recovering from an advanced one. So, try to take care of your diseases in the beggining or you will need medicines or potions to cure you!

3.Medicines, Potions and Blessings
a)Medicines: The player can buy remedies now to help the recovery of the disease. These medicines help a lot in the evolution check, and can be crafted after the player learns how, by reading the “Natural Remedies” book randomly available on most vendors.
b)Alchemy: Initially the disease is unknown to the player. Depending on your level of Alchemy and what medicine books you have read, the disease will be diagnosed. Every disease has a specific potion that is cheaper than generic “Cure Disease” potion. The player can craft them all with the newly added ingredients. Specific “Cure Disease” Alchemy potions still are effective, but they only ensure that the player will pass the next evolution check of the disease. Generic "Cure Disease" potion just increases Disease Resistance for the next evolution check.
c)Poisons: Also, it is possible to buy or craft potions that will cause a disease’s effect on NPCs with those ingredients. Check “Grayfox’ Anatomy” book for more information.
d)Blessing: Praying on altars yield a random % disease resist, but also offers the possibility to cure instantly all the diseases as long a ritual is performed (check “Grayfox’ Anatomy” book for that).

4.Books:
There are two books that detail the disease system. The first and basic one is called “Natural Remedies”, and explains how to deal with diseases. It teaches how to craft basic medicines on the cookpot using common ingredients.

The second one is called “Grayfox’ Anatomy” and explain details of each disease, how to deal with them , teaches how to craft average medicine and give more information on how alchemy and altars can affect diseases. You should read “Natural Remedies” before reading this to earn all the benefits.

There is a compendium for each disease explaining all its details and stages. Reading a compendium after reading “Grayfox’ Anatomy” will teach you how to craft the strongest medicine against that ill.

5.Fatal diseases
Apart from Ataxia and Rattles, all other diseases are fatal, and will kill the infected slowly after the last stage, reducing their health, magicka and stamina until there is nothing left.

6.Random diseases
The player can catch a disease simply by exploring the world now. Exploring some places has a greater chance to infect the player with a specific disease, while others will probably never get you infected with anything. Reasonability is maintained here, since it will be rare that the player will infected like this, and some diseases that require a specific form of contraction, like Sanguinare Vampiris, never are contracted like this.

7.Much more
There are many details I won't include here in this description. Look for more ingame. Load Screens and books have been added for guidance, and some effects have been added to increase immersion and maybe surprise you a little. Have fun!

INSTALLATION:
Install with Nexus manager, or unzip the files in Data folder inside Skyrim’s folder, just like other mods. If you are on Steam, just subscribe it and open the game launcher, then wait the quick download. If you are diseased before activating or updating this mod, you will be given an option to be cured or your diseases! (Mostly to avoid bugs.)
I highly recommend installing the Diseased - Droops Medicine Addon by ezzypixel. He made us all a huge favour on implementing the Droops disease added in Dragonborn DLC, since it was missing in this mod. 

UNINSTALLATION:
Make sure you are not diseased and remove the mod file “Diseased” from load order (or delete it). If any disease is left, you can use an altar after removing the mod and you will be fine.
Or use the MCM menu and choose to uninstall it. Then save and remove the mod file “Diseased” from load order (or delete it).

COMPATIBILITY:
Completely compatible with ANY expansions Dawnguard and Heartfire.
Dragonborn added a new disease (Droops) and this mod didn't implement it. It means that once you get Droops (only possible in Dragonborn's area, as far as I know), you will never ever get rid of it. If that happens, you can remove all diseases using the Diseased SkyUI Mod menu, the uninstall option. I highly recommend installing the Diseased - Droops Medicine Addon by ezzypixel. He made us all a huge favour on implementing the Droops disease added in Dragonborn DLC, since it was missing in this mod. Besides that, this mod has no other issues with Dragonborn.

All you need is Skyrim version 1.6 or higher and you will be fine. I tried to make this mod the most compatible I could. I believe that it is pretty much compatible with any mod around (maybe not the ones that changes diseases), as long as you put it to load after the others.
Works well with Realistic Needs and Diseases. Just load Diseased after RND and make sure you load a game that you are disease-free, or cure yourself deactivating and reactivating in-game RND (via Sugar Ball and accepting the cure).
Works well with Imp's More Complex Needs v0.31 too!.

A HUGE thanks to ezzypixel for making the Diseased - Droops Medicine Addon!

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For those who understand about modding, or those interested in making mods compatible with this one: the entries I changed were the ones below. Any mod that changes those entries must load before this mod, or this one will not work properly.
Magic Effects:
-CureDiseaseEffect
-AlchCureDisease
Spells:
-DiseaseAtaxia
-DiseaseBoneBreakFever
-DiseaseBrainrot
-DiseaseRattles
-DiseaseRockjoint
-DiseaseSanguinareVampiris
-DiseaseWitbane
-TrapDiseaseAtaxia
-TrapDiseaseBoneBreakFever
-TrapDiseaseBrainrot
-TrapDiseaseRattles
-TrapDiseaseRockjoint
-TrapDiseaseWitbane
-WerewolfCureDisease
-VampireCureDisease

Potions:
-CureDisease

Dialogue:
-DialogueGenericVigilantsOfStendarrCureDiseaseTopic

LoadScreen:
-AltarDisease
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Steam Version: http://steamcommunity.com/sharedfiles/filedetails/?id=111451056

Can I interest you in some other mods I have?
Travel Mod: Ever asked why would you spend 1000 gold for a horse in Skyrim? Well, with this mod you will need a mount if you want to be able to fast travel!
Weighted Arrows: makes arrows and crossbow bolts weigh.
Potions Cooldown: Potions that restore health, magicka or stamina will have a cooldown of 5 or 10 seconds. During this time they will be 10% or 20% as effective as they are supposed to be.
Lorecraft - Vanilla Blacksmithing Tutorial Fix: When the blacksmith asks you to craft a dagger (and later a hide helmet), you will get a book on how to do it. That simple.