The fact that being the Doctor’s companion quite often is a curse disguised as a blessing is something that has been explored before in Doctor Who. Moffat has been toying with it all along, and I really like how it all comes to a head in this episode, how the 11th Doctor has to face that truth and do something about it.
Offer someone all of time and space, and they’ll take that too.
The Doctor knows that it’s dangerous, but he keeps doing it, he can’t help himself. He admits that even though potential companions have choice, it’s not a real choice because it’s like offering candy to a child; and seconds after, he’s already inviting the very person he made the admission to to come along.
The series has already explored his guilt about all this, most obviously when he was dying in Let’s Kill Hitler, and he asked the Tardis’ voice activated console (I think that’s what it was called) to show him someone he hadn’t messed up yet, and it showed him young Amelia Pond, before he came back for her. Amy has always seen the Doctor as her hero, a knight in shining armor of sorts, who saved her from the crack in her wall and, probably most importantly, from the boredom of a mundane existence. That Rory came along meant that she could have her cake and eat it too, she could run away with the Doctor while taking along the one thing she couldn’t leave behind.
Rory himself obviously considers the Doctor a friend and cares about him, but the relationship has always been very different, he’s always been more guarded. He is only on the Tardis because of Amy, and from the very first adventure he had with the Doctor and Amy, back in Vampires of Venice, Rory has always been ready to hold the Doctor accountable. He’s always known that this whole thing could end very badly, and he’s along to protect Amy as much as he can… and then some. Thousands of years as the Last Centurion, protecting the Pandorica because Amy was there. Rory loves the Doctor in his own way, but he’s never fully trusted the Doctor. Oh, he trusts the Doctor to get them out of trouble, but he’s always had reservations about what being around him will lead to.
It’s interesting, Rory, the nurse, the soldier, is the one person that the Minotaur in The God Complex doesn’t want, because he has no faith that it can feed on. Rory is the realist, the pragmatist. Meanwhile, Amy had her faith in the Doctor, in her heart she always believes that he will make it all okay, no matter what; and this is the moment when the Doctor realizes that he has to strip away that faith. He has to make her see him as he really is, or as he believes himself to be: a selfish man, who took her along for his own reasons, because he wanted to loved, without any consideration for what it might do to her, for what dangers it might lead her to. The interesting thing is, even though the Doctor has known this all along, he’s never really made himself face it, until he makes Amy believe it. And once he faces this one simple fact, that while Amy is with him she’ll always be in danger, there’s only one thing to do: take Amy and Rory home. Give them as much as he can, but most importantly, put them back in their ordinary lives, where they won’t have amazing adventures, but where they also will be mostly out of danger.
The moment he finally calls her Amy Williams, that’s the moment that he finally, truly lets his little Amelia Pond go.
It’s heartbreaking and very noble of him.
And even though I’m sure no one really believes, watching this, that Amy and Rory won’t be back on the Tardis at least one last time, I didn’t really expect the Doctor to say goodbye in this episode, and I suppose it’s in part because of that that the moment felt even powerful than it was going to be anyway.