This is a really good story. It moved me to tears... I think you really captured the dark side of Sonic, and the competent side of Amy, in a way that very few people are able to pull off...
I do have some criticisms though. You need to show, not tell... Rather than simply state character emotions and thoughts, describe them. Also, you should try to mix dialog and description a little more. Straight he said, she said, he said is a little boring. Try adding some descriptions of their tone of voice, or their facial expressions, as they say those things.
Other than that though... Great story! Like I said, it made me cry. I've been trying to bring out that part of Sonic in my stories for a long time, and I've never been able to. Good job!