
O Captain, My Captain. Even when dealing with writers other than Moffat, I'm very aware of themes playing themselves out in this era of Who. I don't know how much is imposed by Moffat on those other writers, or tweaked once the scripts have come in. Does this story really herald things to come in the rest of the series by virtue of its themes? I can't say. But we have the mirrored tale of two captains (or maybe three if you count the untold story of the extradimensional ship) who let members of their crew down in a time of crisis. The Doctor is specifically called the captain of the TARDIS, so the parallel is there, and carries over to Toby and Rory. Rory, the "son" who almost dies as a result of his captain-father's mistakes. "Ignore all my previous theories" may become an important piece of dialog, not only to show the Doctor's impending failure as a sailor on the seas of time, but perhaps to poke fun at all us fans spinning our weekly theories about the series many mysteries.
Bad writing? So yeah, the episode has some logic problems, the biggest of which may be the Doctor's sudden conclusion that the only way to save Rory is to allow himself and Amy to "die" at the Siren's hands. We're missing a scene or a line there to indicate just HOW he came to that conclusion. There's more, of course, like a pirate that goes missing, the reason Toby would have stayed in hiding for 8 days, and many of the Doctor's slimly motivated decisions, plans and theories. The latter might have a meta-textual reason however. The episode seems to be exploring what happens when the Doctor's quick-draw conclusions prove to be mistaken. Everything he comes up with is disproved by the next piece of evidence. And that's a perfectly reasonable premise for a character who often makes those magical leaps of logic. So maybe the problem is in the direction. That theme, if it's there, isn't clear enough. The logic of the piece isn't sound enough (surprising for a Sherlock writer). The Doctor is just a little goofier than usual, approaching self-parody. And Rory's resurrection scene... Ugh. The Doctor says Amy has to do it because she won't give up, and then... she's gives up. She's given up, and Rory still comes back to life. So I'm inclined to say the direction is at fault, though it really looks like a collaborative failure.
Episodes floating through time. Part of the problem, of course, is that this was originally scheduled to air ninth, i.e. next fall. That certainly explains flashbacks to the previous two episodes, and the Doctor scanning Amy for pregnancy again. As originally envisioned, these would have proven appropriate reminders in 4 or 5 months. As aired, they make the Doctor obsess over the point, and seem like unnecessary padding. Still, they do reveal some things. The current crew will remain intact at least until episode 10 (a relief!), and no revelations regarding Amy's baby or the Doctor's death are forthcoming until the series finale.

The other universe and Amy's pregnancy. Let's now look at some of the ongoing mysteries of Series 5-6 and how this episode might connect to them. After RTD's "inaccessible parallel universes", we now have (in the rebooted universe) intersections where you can apparently walk from one dimension to the next (here via reflections or the Siren). The intersection sits astride two universes, and one can see interior of the pirate ship from the space ship's windows. In this same episode, we get another disturbing visit from the Eyepatch Lady and a reference to Amy's phantom pregnancy. That tells me there's likely a connection. Is Amy's womb another of these interdimensional intersections? Is she the focus for a universe in which she had a baby, and another where she did not? Is that why pieces of the other universe (Mrs. Eyepatch) keep bleeding through? To be continued, but the explanation for other dimensions given here may well prove important.
Is the TARDIS sick? Taken at face value, the intersection messed with the TARDIS and it ran to the other dimension. Looking at it from another angle, everyone who was brought over by the Siren was sick or injured. We didn't see the Siren take the TARDIS, but might she have attracted it across the veil of worlds? It is next found behind a shower curtain in sickbay. It's probably nothing, but we still don't know what made the TARDIS blow up, and she might still have something in her system.

This is Gallifrey. Murray Gold's "This Is Gallifrey" music cue plays over the pregnancy scan. Only musically appropriate to the scene, or is it THEMATICALLY appropriate as well? We already (think we) know that Amy's daughter can regenerate like a Time Lord. Does the music cue confirm a closer relationship? Is she a Time Lord? Will she become one? Or even more intriguingly, is Gallifrey somehow involved? I've read the theory that the death of the Doctor, seen again in flashback here, features a wave of energy that flies across the lake and, presumably, passes through Amy. Is this what affected Amy's pregnancy? Gave the baby regenerative powers? (The Doctor was regenerating.) Shunted it to another dimension? (And does that mean the dead Doctor belongs to another timeline?)
Rebirth of the Time Lords. Rumors abound, especially with the regenerating tot in the mix, of Moffat bringing back the Time Lords, albeit as a young race. It would totally be his style to timey-wimey Gallifrey so that its birth occurs after its destruction. You can play the game at home by tracking down the Doctor's loose DNA, fair play after River's "a single cell would change the world" speech in The Impossible Astronaut. Everything you do of course leaves DNA behind, but even when you look at only those instances where the Doctor's DNA is specifically mentioned, you'll find some. We now have Amy's regenerating daughter and Jenny flying around up there. The Siren just took a circle of the Doctor's skin. It's used to meddle with the human Daleks. Torchwood had his hand for a good while. Are these seeds being planted?
Spoilers: Next week's trailer. If you thought "The Doctor's Wife" was going to be the big River Song reveal, well, I guess you were as wrong as I was (or like me, very conscious of not looking at spoiler information). However, the episode is by comics wunderkind Neil Gaiman, not Moffat, so there goes River. From the preview, it looks positively insane, like something out of Gormenghast, and then green-eyed Ood show up. I'm really curious about this one, and not just because Gaiman wrote it.
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