Shadows of P'Jem
Archer breaks the news to T'Pol about the High Command recalling her from Enterprise. After some discussion Archer tells her he considers her a part of his crew.
Archer: I want you to know I'm filing a protest with the High Command.
T'Pol: That won't make any difference.
Archer: You don't know that.
T'Pol: Captain... I was assigned to Enterprise not simply as an observer but to represent the interests of the Vulcan people. It's clear in the eyes of my superiors I haven't done that.
Archer: They have no right to do this to you. You're a part of my crew.
T'Pol: For another 48 hours. Was there anything else?
Archer: No.
Archer decides to take T'Pol on the mission instead of Trip. He tells Trip he needs to spend some time alone with T'Pol. In the shuttlepod Archer tells her:
Archer: These people have never seen humans before.It makes sense for someone with a familiar face to make the introductions.
T'Pol: I have a lot of work to complete before the Vulcan ship arrives.
Archer: Don't worry - I'll get you back in plenty of time. I just... thought you might enjoy one final mission with your captain. Or maybe I should just take you back to Enterprise.
T'Pol: We're only a few minutes from the capital. Returning to the ship now would be a waste of fuel.
I've heard people bemoan the infamous boob plunge in Shadows of P'Jem. I think it's another Berman and Braga attempt a humor that, pardon the pun, fell flat for some. The good side of the scene, besides getting to see Archer and T'Pol tied together by rope and squirming around in funny positions, is the conversation they have while tied together.

Archer: You're not responsible for what happened. You didn't have any idea that your people had installed a listening post. Or that there were Andorian commandos there.
T'Pol: Enterprise had no good reason to visit a Vulcan sanctuary. I had the opportunity to protest but I chose not to. It's clear that living among humans has caused my reasoning to become compromised.
Archer: I think I understand. You're running away because you're afraid to become one of us.
T'Pol: I am not running away.
Archer: Then why aren't you fighting this transfer? Your people took something away from my father that meant a lot to him. They're not going to do the same thing to me.
Archer and T'Pol escape with the help of Shran, Trip, and Reed. A confrontation between the Andorians and Vulcans leads to T'Pol blocking a phaser blast from hitting Captain Sopek.
Archer: Let's get her to the ship.
Sopek: She's no longer your responsibility. We'll treat her on the Ni'Var.
Archer: She's still my science officer.

Archer carries T'Pol back to the ship. When she wakes, he and Phlox help her up. Archer informs her that Sopek will talk to the Vulcan High Command about the transfer order.
My thoughts: Archer is insistant on keeping T'Pol. These line I think sums up why: "Your people took something away from my father that meant a lot to him. They're not going to do the same thing to me." T'Pol means a lot to him. I think in his eyes T'Pol isn't the Vulcan observer. She's his science officer, his friend, and maybe more to him.
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