Its called The Metamorphosis of Prime Intellect.

http://www.kuro5hin.org/prime-intellect/

Not sure if anyone here has seen this or not. I read it for the first time a couple of years ago and I reread it once in a while. I don't want to give away any details. Its a well-written story that raises a lot of interesting questions, and the author will actually respond to e-mail if you want to talk to him.

I must caution you: the story contains extreme, graphic depictions of violence and violent sex acts