I only read an excerpt of one paragraph from this story - the villain (a Shoggoth?) admits to having engineered all of human civilization (agriculture, industrialization, etc) purely with a view to humanity's greater downfall (at the hands of the Old Ones?).

I think I read the excerpt online, maybe in a review and this was a few years ago. I believe the story (I suspect it was a short story) was in print.

I thought that the story was `Fat Face' by Michael Shea, but this turns out not to be the case.

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    When did you read it? Was it online? Anthology book? Magazine? Ancient runes on megaliths? – FuzzyBoots May 19 '16 at 19:53
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    IT couldn't be a shoggoth, they have no brain usually... on the other hand that would explain a thing or two about us. – Yasskier May 19 '16 at 21:55
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    @Yassiker: Old One 1: "Those Shuggoths couldn't possible be intelligent and trying to destroy us. Right? Right?" Old One 2: "Tekeli-li." – Buzz May 19 '16 at 22:26
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    According to Lovecraft's mythos, all current life on Earth is the result of industrial waste runoff from the Old Ones'. – Joe L. May 19 '16 at 23:01
  • purely with a view to humanity's greater downfall – What exactly do you mean by this? Did the villain help mankind such that it downfall would be more spectacular? Or did the villain steer humanity to fall, when it wouldn’t have fallen without his “help”? — Also: To whom does the villain admit? – Wrzlprmft May 20 '16 at 17:46

That doesn't sound much like Lovecraft; his stories generally have humanity as being fairly unimportant to the greater Gods/aliens/etc.

That said, this kinda sounds like The Shadow out of Time. I've put the plot below. The reason I think it sounds kind of similar is because, at one point, the protagonist talks with other beings who have been taken over by the beings in the story (his mind is transplanted into their 'time' while his body is taken over by one of the aliens). I recall him having conversations, possibly about the aliens greater plans.

Here's the plot: https://en.wikipedia.org/wiki/The_Shadow_Out_of_Time

The Shadow Out of Time indirectly tells of the Great Race of Yith, an extraterrestrial species with the ability to travel through space and time. The Yithians accomplish this by switching bodies with hosts from the intended spatial or temporal destination. The story implies that the effect, when seen from the outside, is similar to spiritual possession. The Yithians' original purpose was to study the history of various times and places, and they have amassed a "library city" that is filled with the past and future history of multiple races, including humans. Ultimately the Yithians use their ability to escape the destruction of their planet in another galaxy by switching bodies with a race of cone-shaped plant beings who lived 250 million years ago on Earth. The cone-shaped entities (subsequently also known as the Great Race of Yith) lived in their vast library city in what would later become Australia's Great Sandy Desert (22°3′14″S 125°0′39″E).

The story is told through the eyes of Nathaniel Wingate Peaslee, an American living in the first decade of the 20th century, who is "possessed" by a Yithian. He fears he is losing his mind when he unaccountably sees strange vistas of other worlds and of the Yithian library city. He also feels himself being led about by these creatures and experiences how they live. When he is returned to his own body, he finds that those around him have judged him insane due to the actions of the Yithian that possessed his body. While he was experiencing a Yithian existence in Earth's ancient past, the Yithian occupying his body was experiencing a human one in the present day.

The narrator at first believes his episode and subsequent dreams to be the product of some kind of mental illness. His initial relief at discovering other cases like his throughout history is withered when he discovers that the other cases are too similar to his own to be without a connection. The narrator's dreams become more vivid, and he becomes obsessed with Archaeology and Ancient Manuscripts (as was the Yithian) - but lacks any sort of proof that would demonstrate whether he was (or is) simply mad.

He discovers that the Yithians on Earth died out eons ago, their civilization destroyed by a rival, utterly alien pre-human race described as "half-polypous" creatures, but the Yithian minds will inhabit new bodies on Earth after humanity is long gone. His tenuously held sanity is challenged when he discovers the proof he seeks—and that not only do remains of the Yithians' past civilization still exist on earth, but also still remaining are those who destroyed them. It is also mentioned that the current appearance of the Yithians is not the original, but one acquired during a previous mass-projection of the minds of their race when disaster beckoned, leaving the original inhabitants to die in the bodies of the Yithians.

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