At Area 51, the Doctor is in a straight jacket and slowly being encased in the "perfect prison," a box that's just too similar to Season 5's Pandorica. Canton arrives and tells the Doctor that he's found Amy, but suggests she's no longer among the living and wants to know why she was keeping a tally. The Doctor, now beardy, replies "Why don't you ask her?" This pattern repeats for the rest of the teaser as Canton tracks down the Doctor's friends, the "perfect prison" gets more complete, and the bodies pile up.

When the prison is finished, Canton brings in the body bags and locks the door. Now inside the impenetrable cell, all the time travelers escape their bonds and enter the cloaked TARDIS. They rush off to save River from her jump off a New York skyscraper where she just escaped from Canton weeks earlier (ah, time travel). Reunited, the Doctor tells them that they have a secret weapon: "Neil Armstrong's foot."

Now, while I enjoy everything "Day of the Moon" sets up, it doesn't quite resolve the story that began last week. Instead, it throws more machinations and plots into the air, many of which won't be resolved for months. Example: Following the credits, the Doctor reminds Canton that they needed the three months for everyone to learn as much as they could about their new enemy. So Canton's chase of the companions was a ruse, but it doesn't explain why the Doctor needed to penned up for all that time. I could be thick, but the purpose of the "perfect prison" never becomes clear. Was it just an obscure part of the plan or something more?

The group splits up again, with Amy and Canton following the path of the child in the spacesuit. It leads to an orphanage in Florida where the caretaker, Dr. Renfrew, believes that it's sometime earlier in the decade. Confronted with the truth, he just responds with, "Yes, that's the plan," and reiterates that the facility will shut down in 1967. The walls are lined with the words "Get out!"

No, wait! Sorry, time for an out-of-sequence scene. Canton recalls a moment in the TARDIS when the Doctor explains they've all been injected with telepathic recorders in their palms. If they should see one of the creatures, they should record the incident and describe it. The device will glow red, indicating that they've left a message for themselves. All of this must be done because, as Rory puts it, the aliens "self-edit" themselves out of people's memories. Writer Steven Moffat used a similar memory-lapse concept in last season's second episode "The Beast Below," and I doubt it's an accident.

With another writer, reusing such an idea could be seen as lazy, but Moffat makes it work in a smashing scene in which Amy finds a horde of the creatures hanging from the ceiling, fast asleep,  in one of the orphanage rooms. She tallies herself and records a message to get out. After fighting with her own memory and nearly waking the creatures up, she escapes. The scene is tense and one of the best executed of the Matt Smith era to date. Kudos to director Toby Haynes for realizing it with such confidence.

The Doctor, meanwhile, makes a few adjustments to Apollo 11's command module.

Elsewhere in the orphanage, Amy finds a room with an observation hatch. It opens as a woman with a cybernetic eye looks out into the corridor. "No, I think she's just dreaming," she says before slamming the hatch shut. If this isn't an echo of things to come, I'll be shocked. Amy walks in the room, but finds the hatch and the woman have disappeared. Instead, she finds an ordinary bedroom with photos of the girl on top of a dresser; included in the array is a picture of Amy holding a baby. Before she can process what she's seen, the girl arrives still in the spacesuit. She repeatedly asks the girl to tell her who she is, but the creatures arrive and whisk Amy away.

Canton learns from Dr. Renfrew that "it is important" that the girl be looked after. He also manages to shoot one of the aliens, which tells him that "We have ruled this planet since the wheel and the fire." Yeah, that's pretty ominous, even for a Doctor Who villain.

The TARDIS materializes at the orphanage, where they find Amy's telepathic recorder and the injured creature finally gives the Time Lord a name to his opponents: The Silence.

I should probably mention that Rory is pretty much a bag of nerves from this point on. He clutches Amy's recorder worried that she may die and that she really loves the Doctor. I guess it doesn't help that Amy keeps asking for the guy with the bow tie. Since the time of Moffat's utterly brilliant third-season story "Blink," I've wanted to see a couple traveling in the TARDIS and making their relationship work despite the rigors of adventuring through time. I keep hoping Amy and Rory will be that couple, but as long as the show keeps falling back on this romantic triangle business, they can't get to anything fresh with the concept. Luckily, the episode seems to address that issue in a subsequent scene.

The Doctor, Rory and River return to the warehouse from the previous episode, where they examine the spacesuit; it's been modified with alien technology. It keeps the girl alive, but she's ripped her way out of it. As the Doctor puts it, she's "incredibly strong and running away. I like her." Now on her own, the Doctor expects the girl will find them.

At the prison, the injured Silence tells Canton that, "You should kill us all on sight." Luckily, he records the encounter on Amy's phone and sends the video to the Doctor.

After a brief conversation with Rory about his centuries long wait for Amy, they run off to that odd TARDIS-like control room to rescue her. The Doctor accomplishes this with Rory, River and a television set. The Doctor notes he's seen one of these control rooms before, but shrugs it off to show the Silence just how clever he is. Oh, he also flirts with River before showing off his brilliant solution: inserting that bit of video where the injured Silence said "You should kill us all on sight" into the moment Neil Armstrong set foot on the moon. With the Silence's natural ability to insert post-hypnotic suggestion before erasing a person's memory, the video stands as a kill order that will last thousands of years. Rory gets Amy free and into the TARDIS as River kills the nearby Silence.

Wrapping things up, the Doctor tells President Nixon to let Canton get married to his boyfriend, who also happens to be black. He also lets the president know that "Tricky Dick" will never be forgotten in the annals of history. The TARDIS lands in the 51st century, returning River to her storm cage. She gives him a passionate kiss, but it comes as some shock to the Doctor. River, in turn, is surprised to learn that this moment is the first time he received a kiss from her.

In the TARDIS, Amy and the Doctor discuss her almost-pregnancy. The key thing: She was worried that carrying a baby through time might have a strange effect on it. Again, the dialogue plays on the possibility of a romantic triangle, but it just as quickly defuses it when Amy calls out to Rory over the recorder. I still worry the show may go down this route, but Moffat seems to indicate that he's aware of the danger in such a storyline.

The scene cuts to New York, sixth months after the moon landing. The coughing little girl emerges from an alley and tells a concerned homeless man that "It's quite all right. I'm dying, but I can fix that." She then proceeds to regenerate!

All things considered, "Day of the Moon" is more set-up for the season arc than a satisfying conclusion to a two-part adventure. While it seems the Silence have been defeated, we will no doubt see them again. It kind of robs the Doctor of his victory and dampens the menace.  Ultimately, Canton feels extraneous. He learns about time travel, aliens and the like for reasons that are still not clear. The Doctor even drops him off at Area 51 so he can finish the story without the man in black cluttering up the set. While his presence at the Doctor's funeral suggests there's more in store for him, he seems to get cast aside in concluding moments of the episode.

Canton and the Silence are the examples of the season arc getting in the way of the story. The show is playing a long game and it could damage the enjoyment of individual episodes. Since returning in 2005, the writers allowed a key phrase to chase the Doctor across time and space, creating the loose season storyline. With the cybernetic woman, the regenerating girl, and Amy's possible pregnancy, it appears something much more grandiose will tie the year together and I wonder if the format will actually allow it.

Lessons learned:

President Nixon wasn't all bad. He took on the notion of time travel without starting a clandestine government agency with a ridiculous name to combat some perceived threat.

Amy loves Rory. No, really, she does. Honest.