To be clear, the rogues in this particular case are not the religious order known as the Silence, but the lightbulb-headed, chewing-gum-faced beanpoles in suits that you can’t remember having been scared of, once you’ve stopped being scared of them.
The Silence were an incredibly apt alien for the Doctor and his friends to encounter as a result of the show being filmed in America. Not because there is anything particularly apple-pie or hamburgery about them, but because of Franklin D. Roosevelt’s famous maxim: “the only thing we have to fear is fear itself.”
When you consider what it is that makes the Silence such an icky proposition, it’s not so much that they hang upside down like bats (although that’s part of it), or that they point with their long, thick fingers and do that sucky thing which kills people (although that is also part of it), or that they look like Edvard Munch’s painting The Scream, if that painting was inducted into the Men In Black, and then developed an eating disorder (another part of it), it is chiefly the fact that they live in the bits of your life you don’t pay attention to, and hide there in plain view.
Just as the Weeping Angels only attack when your body does the involuntary things it has to do naturally – blink, sleep, run away – the Silence make sure they only linger in the part of the brain that erases sensory information it deems to be irrelevant for storage, an occupation of the darkest recesses of your mental filing system. And it would be fair enough to ask why it is a scary thing to be co-erced into doing stuff by an alien force that you can’t remember being frightened of, but that’s not the key thing. The key thing is the disquiet they leave behind.
Remember being sure of that thing you thought you knew for certain, and then finding out you were totally wrong? Remember that worry as you started to wonder what you can have been thinking about when you first learned it? Remember idly wondering if you were losing your marbles? That’s where the Silence live, they are disquiet made flesh: the only thing you have to fear is your own unease.
And of course, they look like The Scream because that’s how humans would expect that feeling to manifest physically.
Of course, a sci-fi romp about the fear of being a bit ditsy is no sci-fi romp at all, so it turns out they’ve been parasitically forcing humankind to evolve, to fly to the moon, so they can use the NASA spacesuit. And having been discovered, they start killing people, chasing Amy, River, Rory and the Doctor, forcing them to draw a tall of Silence encounters on their own bodies, and showing themselves to be the rotters they truly are. Thankfully, the Doctor has footage of a Silent saying “you should kill us all on sight” and having been raised to do exactly what the Silence demand, without questioning it or remembering it, that’s exactly what humanity does.
As a side panel to this story, it’s interesting to note that the 1969 moon landing marks the end of humanity’s state of co-dependence with the Silence, after having helped humans evolve from cavemen to spacemen. That space programme is still widely considered to be mankind’s greatest feat thus far, one that hasn’t been bettered since, so you can read the story of the Silence as a critique of governmental investment in science, since those heady days. Given the freedom to act according to our own agenda, we stop pushing to get to the stars and get back to bickering about theology.
Mind you, we were doing that anyway, so it’s probably a fanciful interpretation
But as we are speaking of theology, the other side of the Silence is their involvement in the religious order that also bears their name. This part of the story is unfinished, so we can’t draw any concrete conclusions just yet. A prophecy exists that says “silence will fall when the question is asked,” and it turns out this question, the oldest question in the universe, is “Doctor who?” The Doctor has to answer the question, and this is when the really bad stuff will happen, so to prevent this, the Silence (religious order) develops an army, led by Madame Kovarian, devoted to killing him.
They even steal Amy and Rory’s baby, Melody, and condition her to become the Doctor’s assassin. This is thwarted by the Doctor, who remains at large, albeit at a low profile, and presumably the question will be asked at some point and he’ll answer it and then LORD knows what will happen.
Or if anyone involved will remember anything anyway.