"Shoggoths in Bloom"

by Elizabeth Bear
originally published Asimov's March 2008

In this setting, shoggoths are a well-known aqauatic species, and no more feared than other dangerous sea creatures.  Prof. Harding is studying them.  They have an odd habit of sunning themselves on rocks, sprouting strange nodules.  Harding samples some. 

He begins to have strange dreams.  In them, he is "eaten" by a shoggoth and becomes one with their consciousness. He comes to understand them as a race that was created for slavery, without the ability to think for themselves.  They are looking for someone to be their master again. 

WWII is brewing in Europe.  Harding knows the shoggoths could be a terrible weapon against the Axis.  However, he chooses to give the shoggoths the command they've been asking him for.  He orders them to be free and learn to think for themselves. 

Well, its certainly a unique take on the shoggoths.  Beyond that, its a well-written sci-fi story.  But hardly a classic.