Hot Zone (S1: E13)
Teyla: If this was really a fight--
Sheppard: If this was really a fight, I would have shot you by now.
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I love the male/female, Sheppard/Weir reaction to the scientist trying to escape the virus. Weir is all: wait, we got it, and trying to talk to the scientists. Sheppard is all: let me go, we gotta stop him.
I don't know why, but I love it when Bates obeys orders from Sheppard instead of Elizabeth.
Elizabeth is so hurt and angry that Sheppard undermined her authority. It's sad. Teyla, as always, is the voice of calm. She goes with Sheppard, following him, but she gently reproved him for his choice to pull rank.
Once the scientists exposes everyone and Atlantis initiates a lockdown, Elizabeth rips Sheppard a new one. By not following orders, by being reckless, Sheppard has gotten everyone exposed. That is a new hole ripped in his soul. Elizabeth is hurt because Sheppard just proved he didn't trust her. Sheppard is forced to realize that his recklessness, his attempt to do everything, may just get a bunch of people killed. That's a hard pill to swallow.
Sheppard's response to endangering others is to courageously put himself in danger to save them.
I love how Weir when she confronts Sheppard isn't so much, "I'm in charge!" spewing tyrannical authority, as she is, "You have to trust me." I think that's what got through to Sheppard because he does trust her. He just didn't act like it, and that hurt her. And he sees it, he sees that he acted without trust.
It's different than when Rodney breaks Sheppard's trust. It's Sheppard basically acting autonomously and proving he doesn't trust anyone but himself and Elizabeth calling him out on it. That is so significant in Sheppard's growth as a character.
Also, in Childhood's End, we have this conversation:
It was really necessary, and Sheppard willingly sacrificed to defend and protect his people.
