Your kindness to this kitten was the most wonderful thing that ever happened to him in his short life. He knew that someone cared, that he was safe, and that he had food available if he wanted it. I am so sorry that this happened and I agree that there was much more going on; I have lost young kittens from feral litters to seemingly mysterious causes. You did everything you could for him and his passing was peaceful and calm as opposed to what it might have been alone outside.
