Yay! I'm so glad you recced this. I liked it a LOT when I read it. It's not just the AU aspect...it's that Major Jackson is SMART. Smarter, in fact, than most of the bad guys on the show. Several times, I predicted what would happen next, and the author (and the Major) outsmarted me. I agree with you that the second story doesn't quite measure up - I felt like it was written just for the sex.
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