Whatever the actual physical cause may be, Kurtz's illness is a metaphor of the disease of the spirit that has overtaken him and, by extension, the whole imperialist effort that is at the heart of the story.
When Marlow first arrives at the colonial outpost, he observes the illnesses prevalent among the "native" workers in the camp, and that no one is doing anything to help them. This is a form of concrete evidence of the abusive conditions upon which imperialism is based. The material conditions in camp, the inefficiency, and the fact that equipment is lying about unused are all signs of the dysfunctional dynamic that governs the situation.
As the saying goes, whatever goes around comes around, and it's inevitable that the colonialists themselves will suffer...
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