Once I figured out that it's actually doing the faction missions that determines when your pill bottle goes empty it changed the way I play the game. The sickness level is plot dependant, meaning it is triggered by main missions only. You cannot change the current level by your actions regarding taking the pill or wait it out.
![far cry 2 no malaria mod far cry 2 no malaria mod](http://majorslack.com/pics/screenshots/farcry2_mac10_02.jpg)
I have no idea if it affects your stamina, but the sickness level is irrelevant. If you refuse to take the pill, 3 more attacks will strike you, the last of which will put you to the ground forcing you to take the pill. During that time you will never run out of pills. Two, no underground job pending (obviously). When stricken by malaria without having any pills left, you will have 3 more attacks coming, the last of which will take you to the church (during campaigns in the north) or the hospital (in the south). Now you're on your second last pill, only one left in the flask, until you get resupplied.
![far cry 2 no malaria mod far cry 2 no malaria mod](https://m.media-amazon.com/images/M/MV5BYTlmYTMwYzMtM2M3OS00NDJjLTg3NjgtYjUyN2JkMDY4ZDVhXkEyXkFqcGdeQXVyNzg3NjQyOQ@@._V1_.jpg)
Upon completing such main missions, you'll find an entry in your book asking you to find someone who provides you with medicine, showing that underground mission symbol.
![far cry 2 no malaria mod far cry 2 no malaria mod](https://i.ytimg.com/vi/QU5P5c5C4ms/maxresdefault.jpg)
One, an underground job is pending (triggered only by some main missions). I've had my share of malaria myself, let me share my experiences with you. *mumbling to myself, how could I have missed this thread?*