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[Sphalerite]

I don't understand why the hospital isn't equipped to handle infections like this.

What exactly are they supposed to do about it?  Until dwarven penicillin is invented, there's not much they should be able to about massive systemic infections.  Amputating the rotting part doesn't help when the entire body is rotting.  Applying magma you don't need the hospital for.

[Funburns]

I don't understand why the hospital isn't equipped to handle infections like this.

The player is. The most effective anti-plague method used before the 19th century was the quarantine. Badger-pastures and burrows allow the creation of a leper colony in one of those huge, played out mineral veins lying around the bottom of your fortress. Create a drop zone above them to give any perpetually-infected survivors seeds and a water pond for them to fertilize the rock and start farming operations. Give them a pick and seal off the colony for good.

Other, related preventive measures include blocking the caverns off when there's an FB alert and never letting it touch anything other than the elaborate, lever-operated trap you constructed just to deal with these things, or walling off the infected ward of your hospital and drenching everyone with magma. You might want to spoon some magma onto all the places the infected walked over, too.

There are also the "die trying" and "cheat" options.

[Sutremaine]

You can build floors or walls over patches of contaminant.

[Umune]

If a dwarf has no feet, will Urist get the infection from walking over the contaminant?

[Sutremaine]

Yes, because the dwarf is still in contact with the floor.

[Eric Blank]

He'd probably get infections all over the place since he's now crawling around.

[thijser]

Trough you may have been lucky. Not all secretions will spread some seem to disappear before they are spread. If this is the case you are very lucky and only the infected once will die. Go to the health screen to see if you were lucky (if only the badgers are infected and they are still the only once infected your are lucky).

[Trekkin]

I've been experimenting with decontamination showers for just this reason. My current design douses the carriers with magma briefly first, then water (once the magma's pumped away) to put out the fire that sometimes burns away the FB blood. I repeat the process three times before I let FB combatants back into the fort proper.

[dogstile]

Wait, these infections can still destroy an entire fort?

Ugh, suppose i'm still waiting for the version where you can deal with them without having to write off large amounts of your population.

[Golcondio]

Wait, these infections can still destroy an entire fort?

Ugh, suppose i'm still waiting for the version where you can deal with them without having to write off large amounts of your population.

Pray, sir, what would be the Fun in that?

[dogstile]

Wait, these infections can still destroy an entire fort?

Ugh, suppose i'm still waiting for the version where you can deal with them without having to write off large amounts of your population.

Pray, sir, what would be the Fun in that?

I name all of my dwarves after my friends. I find it annoying when they all get killed due to some bullshit infection that can't be cured.

[Ultimuh]

Wait, these infections can still destroy an entire fort?

Ugh, suppose i'm still waiting for the version where you can deal with them without having to write off large amounts of your population.

Pray, sir, what would be the Fun in that?

I name all of my dwarves after my friends. I find it annoying when they all get killed due to some bullshit infection that can't be cured.

Welcome to Dwarf Fortress. The game where your fortress is screwed, no matter what you do. 

[Necro910]

Wait, these infections can still destroy an entire fort?

Ugh, suppose i'm still waiting for the version where you can deal with them without having to write off large amounts of your population.

Pray, sir, what would be the Fun in that?

I name all of my dwarves after my friends. I find it annoying when they all get killed due to some bullshit infection that can't be cured.

There is a cure.

Spoiler (click to show/hide)

Excessive amounts of magma, applied directly to the forehead!

[EBannion]

If you reclaim a fort that died to the plague, will the incoming dwarves catch it too? Or does the lose - reclaim process clean up the ick?

[Sutremaine]

The stuff sticks around. See the reclamation of Battlefailed, and the fate of the first few children to be born there...