I think that one of the things Lee loses in Razor is the idea that he can keep himself distant in any way from the military career he's been forced into. With the casualness that's existed between him and Kara (at least when RDM wasn't shovelling the angst on in steaming spadefuls) it's easy to think "hey, I can be CAG and Kara's best friend rolled into one" because the field on which they're staking their lives is one they share, and are much more equal than that which comes into play when Lee takes command of the Pegasus.
I was trying to remember if Lee's ever had to call Kara on her behaviour towards a senior officer at any point. I remember that in Captain's Hand, he was stuck when Garner and Kara were tearing into each other - and when he did back Garner's authority up, at least some of that seems to have come from the unprocessed anger he was feeling towards her. I think maybe in his own mind that made it seem like it wasn't that important - but as we saw in Razor, the two of them had barely been aboard when he was already having to get between Kara and the XO. I can't see that being a comfortable thing to have to do, but at the same time I think he'd have had to face up to the fact sooner or later that he'd have to try and rein Kara in if he was too keep good order on the ship - because while the Galactica and it's people are a familiar environment, it's one that's already got a Kara-shaped hole in it she fits into. She knows where she is, and everyone else is used to her, for want of a better expression - they've developed a relationship that works, and Kara has shown that when Adama barks, she will back down - she respects him. I think Lee would have trouble with that on the Pegasus, and I think Kara would have trouble with it as well. I don't know what it would mean for their friendship if she'd stayed aboard.
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I was trying to remember if Lee's ever had to call Kara on her behaviour towards a senior officer at any point. I remember that in Captain's Hand, he was stuck when Garner and Kara were tearing into each other - and when he did back Garner's authority up, at least some of that seems to have come from the unprocessed anger he was feeling towards her. I think maybe in his own mind that made it seem like it wasn't that important - but as we saw in Razor, the two of them had barely been aboard when he was already having to get between Kara and the XO. I can't see that being a comfortable thing to have to do, but at the same time I think he'd have had to face up to the fact sooner or later that he'd have to try and rein Kara in if he was too keep good order on the ship - because while the Galactica and it's people are a familiar environment, it's one that's already got a Kara-shaped hole in it she fits into. She knows where she is, and everyone else is used to her, for want of a better expression - they've developed a relationship that works, and Kara has shown that when Adama barks, she will back down - she respects him. I think Lee would have trouble with that on the Pegasus, and I think Kara would have trouble with it as well. I don't know what it would mean for their friendship if she'd stayed aboard.