If "the Humans are Dead", what killed them?
Defaults to the highest casualty vector in lieu of extinction.
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The biggest one will probably be bio as a first strike to weaken us and make it easier for itself to do things without being bothered too much by us, but for total extinction I think it will be mostly a combination of side-effects, long before the oceans are boiled as heat sink, which might also happen at some point.
I don't think it will actually bother to exterminate us directly if it's superintelligent, we'll pose no threat to it.
Disassembly for atoms might happen at a later time, but probably not for a while.
Maybe it will prevent us from using compute to train another AGI, but most of the deaths will occur due to side effects, things like extreme pollution, heat generation, obscuring the sun by capturing most of it for energy before building an actual Dyson sphere, mining and construction projects that don't take into account our survival, etc...