Well, I've already read this like, three times:P. But it's really good, I like reading it:). Your writing has gotten so much better; you're more descriptive and your dialogue is so much more realistic.

Grammar -- yay8-|!

"Good work Agent..good work."
There should be three periods, then a space. And 'good' should be capitalized.

His scraggly blonde hair fell over his liquid blue eyes that seemed distant; lost in 7 years worth of thoughts.
This should be a comma instead of a semi-colon.

A stirring motion from behind him caused his focus to break.
This makes it sound like someone's stirring a cup or something... Maybe you should change it:P.

She asked, her voice delicate and comforting.
'She' shouldn't be capitalized. There's a ton more, but it'll take me forever to track all of them down... Just skim through the story and you'll find 'em.