Chronic Disease (3.5e Flaw)
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More than one disease can be picked at once. You cannot ignore, remove, or overcome their effects by any means, not even by a Miracle or Wish spell, or by achieving disease immunity of any kind. Their effects are very different from those of common diseases (no ability score damage, sometimes). The effects of these diseases stack. If you picked two diseases that gave a -2 penalty on Strength checks, then you would actually take a -4 penalty on said checks.
Note that any of these flaws should be discussed with your GM and considered properly, since they can be really difficult to handle.
Anterior Hypothalamic malfunction
Your brain is unable to effectively control your body temperature. Whenever you are in a cold or hot environment, roll 1d4 + half your Constitution modifier. The result is the number of hours you have before you start feeling weak due to thermic issues. You become shaken, and after 10 minutes or taking an extenuating action, you faint. If your temperature is stabilized by someone else (Heal DC 12 or Survival DC 15, each of which takes 30 minutes), you recover consciousness after 1d4 hours. Otherwise, you will remain unconscious until the environment you reside in is no longer hot nor cold.
Your heart rate works at a considerably lower frequency than normal and necessary. When you are put through heavy physical effort, you feel weakened, and sometimes, you faint. Whenever you fail a Strength check, or Constitution check to hold breath, hustle or sprint, you become staggered, as if with taking non-lethal damage equal to your max HP. After 2 rounds, you can make a Fortitude save (DC 15). If you fail that save, you faint for 1d4 hours. Also, if you become staggered due to your bradycardia and keep trying to push yourself (by failing a Strength check, or Constitution check to hold breath, hustle or sprint), you automatically faint after 1 minute, if you don't have success in the Fortitude save (DC 15 again), you take lethal damage equal to your remaining hitpoints plus one, and start dying, which is treated as normal. The benefits of diehard feat are not of any use when you are staggered or start dying due to this disease.
You are completely intolerant to gluten. Gluten is contained in wheat, rye, barley and oats. Food based on these elements is pretty obvious. Still, remember beer is made of barley (though there exist other kind of beers, like corn beer, which are fine for people with Celiac), but mead isn't. Gluten is treated as a poison, it acts about one day after ingestion. This "poison" allows no save, and the initial damage dealt to ability scores is the following: 1d3 Con, 1d3 Str, 1d2 Dex and 1d2 Cha. You also take, a -2 penalty to all skill checks that require concentration for 12 hours. This "poison"'s secondary damage occurs 1 hour after the initial damage, and it is intestinal upset: you'll have to run! This "poison" leaves your system after this. The ability score damage heals over time as normal.
When you are taking initial poison damage, you can make a Heal check (DC 20) to identify the cause of your symptoms.
You are unable to produce insulin, and therefore depend on obtaining it artificially. Every day, you must consume a dose of insulin, or take 1d4 Con damage and 1d2 every other ability scores damage. A dose is consumed by injection, which can be administered by you or another person with a succesful Heal check (DC 15). The dose is lost if the Heal check is failed, and if it's failed by more than 10, you are also dealt 1 point of lethal damage. A dose is sold in any decent apothecary, and is worth 10 gold pieces. If your Constitution score is 16 or higher, you need an extra daily dose. And for each 5 total HD you have, you need one extra daily dose (one extra dose at 5HD, two extras at 10HD, and so on). You can never become addicted to insulin in any way, not even magically. You will never need more than 4 daily doses, no matter how high your HD is, and taking two doses within the same 2 hours will lead to the same ability scores damage as if you hadn't taken it for a day. Your Intelligence score can't drop below 3 due to Diabetes symptoms or insulin abuse.
Your kidneys dry easily, which occasionally leads you to terrible, long-lasting and distracting pain. You must consume half a gallon of water a day. If any day you fail to take the full amount of water needed, you receive 1 point of lethal damage per HD you have. If you fail to drink at least half the needed amount, you receive 1 and 1/2 points of lethal damage per HD you have. If you take damage in any of these two ways, you also take -2 penalty on all skill checks and attack rolls until next day, and any water you drink until you sleep is useless to the Dry Kidneys disease cause. The next two days, you'll have to compensate the liquid loss by drinking at least three quarters a gallon each day, or suffer the same consequences for failing to take the full or half amount.
Your defenses against pathogens are extremely weak, making you hugely susceptible to other diseases. You receive a -10 penalty on Fortitude saves against diseases. When a disease afflicts you, add +1 to any hit point or ability damage it deals. For example, if it normally deals 1d6 Con damage, it will deal 1d6+1 Con damage to you instead. The incubation time for any disease you take hold of can be no longer than 1 day. You can never get rid of the disease by your own natural means, given your immune system is almost non-existent.
Your lungs are slightly malformed, which give you some troubles related to breathing. When making checks to keep running, hustling or holding breath, treat your Constitution score as 4 points lower than it actually is. Also, the Endurance feat numeric bonuses are all halved for you.
Severe Pollen Allergy
You are easily afflicted by your allergy to pollen. When you are in a forest, jungle or plains terrain (or in an urban environment surrounded or partially located in these biomes), roll 1d3. The result is the number of hours before you make a Fortitude save (DC 20). If you have succeed, you gain a degree of allergy. If you fail, you gain two degrees. Roll another 1d3, and repeat this process while you remain in these environments. The max number of degrees is three. Each degree is described below. For healing purposes, consider them as the disease named in each description, while suffering from these, you may make a Fortitude save each hour.
First degree: You start having some respiratory difficulties. You take a -2 penalty to all Constitution checks. For healing purposes, consider this a Mindfire.
Second degree: Your respiratory difficulties become more severe. You also experience a fever. You take -4 penalty to all Constitution checks, and a -2 penalty to Strength checks and Strength-based skill checks. For healing purposes, consider this a Cackle fever.
Third degree: Your respiratory difficulties and fever are alarming. You take a -6 penalty to all Constitution, Strength and Strength-based skill checks, and half that to attack and damage rolls. All your mental attributes count as 6 points lower than they are. If any one of them is now considered as lower than 1, it's not dangerous as commonly considered; you will be completely recovered as soon as you are healed. For healing purposes, consider this the Devil Chills.
There is no way the sickness can go beyond the effects of the Third degree status. If you are targetted by a Restoration spell, you may make a Fortitude save (DC 15), if successful, you will lose one degree of allergy (and may be fully alleviated).
ThrombocytopeniaYour low platelet count makes it difficult for your body to heal its wounds by itself. If damage dealt by an enemy leaves you in negative hitpoints, you cannot stabilize, unless you have the Diehard feat. When you are dealt piercing or slashing damage, you take extra damage of the same type dealt equal to half your total HD (minimum 1). If you take a Bleeding Critical or suffer a similar weapon strike that deals Constitution damage or extra damage through bleeding, you are dealt 1 extra damage of the same nature (or damage per tick if it's a persistent effect).