We see Rodney approach Sam, announcing that the ship is good to go. She praises him, then tells him to take Radek back to Atlantis, take a few days off, and get to work on boosting the city’s shields. She’s going to take the ship out; Lorne is in charge of Atlantis for the time being. (Poor Rodney, overlooked again, but in that climate, it’s better to have a military guy in charge, and Sam knows it.) Rodney protests that she needs rest too; she reveals that their intel says that Michael is on the move again. “So let someone else go!” he tells her, but quickly realises that it’s futile to argue with her and reluctantly lets it go. He starts to leave, when she frowns and says “Hey!” He turns back to her, perplexed; she gives him a look (similar to the one his sister gave him back in “Miller’s Crossing”, when Jeannie said she loved him and he had to be prompted to say it back). “Good luck?” he says wearing an expression that suggests that he has no idea what she wants. She gives him a contemplative look of her own, then says, sincerely, “Thanks, Rodney,” and leans in to hug him (awwwwww), adding “for everything.” He looks vastly uncomfortable. (Heh, you’d think he’d be happy to get a hug from Sam; I guess his discomfort with expressions of affection won out over his crush …. Anyway, this scene hit me harder this time than it did the first time watching it — excuse me while I hunt down some tissue ….) Rodney leaves, looking disconcerted, glancing over his shoulder for a moment. (I think he’s trying to laugh it off at first, like What are you getting all sappy for?, but that he then realises that she’s saying goodbye.) We see Sam face the camera, looking like she’s about to cry. (Dammit, where’s that tissue??)
We see the Phoenix take out a hive ship and do minimal damage to another; Sam doesn’t think it worth the risk to try to destroy the other, and gives the order to retreat. Rodney tells John that the Phoenix did wonderfully against insurmountable odds, but that eventually their luck ran out. Michael lured them into a trap with false intel; we see a few hives surround and fire on the Phoenix. Their ship critically damaged, Sam beams the crew to the planet below, then, when the transporter goes offline before she can escape herself (or so Rodney figures), she flies the ship into one of the hives. The resulting explosion takes out the other two. “And we buried another empty casket,” Rodney finishes sadly. (*Sniffle* In the primary timeline, I want Sam to retire and live happily with Jack, of course, but for an alternate timeline? I can’t help but feel a moment of pride for her, albeit tinged with sadness, for her willingness to die this way. Er, not that there was really any doubt that she would; she’s risked her life before. But I like to think that, if she couldn’t beat the bad guys, she’d at least go out fighting and take a bunch with her. Rodney is obviously as proud of Sam as I am as he shares the tale. I feel a moment of sadness for Jack, though.)"