Shoggoths were created millions of years ago on Earth by the Elder Things as their slaves.  They were mindless, shapeless blobs of ectoplasm that toil away under the sea for millennia.   When their masters finally came out of oceans, the shoggoths followed.

Due to the constant warfare between the Great Race of Yith, The star spawn and other horrors from space the Elder Things gave the shoggoths more and more responsibility.  This lead to them developing a bit too much intelligence in free will.   During one of the many wars, the shoggoths revolted.   They struck and uneasy peace with the Elder Things, and it’s been that way ever since.

The shoggoths are globs of ectoplasm.  While they are smarter now than when first created, they are hardly more intelligent than the smartest dog.  And it’s a good thing, as they can control their bodies and form whatever tool, appendage, shape and size needed.   They heal nearly instantly and almost nothing hurts them.   They are almost literally unkillable.
While resembling amoeba, they are not single celled creatures.  Hell, they are not even life as we know it.  They are not made up of matter, they have no distinct form, no organs, and quite frankly, we don’t even know if they are alive in the way we understand it.

No one has ever recorded killing a shoggoth.  The best one can hope for is to delay, distract or to escape one.    It’s a good thing that they don’t have what we would call motivations for if they did, they would be an awesome force.   Instead, they seem to prefer to be left alone.
A few unsubstantiated reports say that there is a small community of shoggoths in hiding that a have assumed some animal form.   If this is true, it’s very disturbing.   Imagine if they had the wherewithal to take long term human form...