In Genesis, the creation of the world is described as the work of six days. Perhaps it's a coincidence that there happens to be six Meditations. Perhaps not. Listing the Six Days might be useful:
- Separating light from darkness
- Separating the sky from the waters
- Separating the dry land from the seas; sprouting vegetation
- Separating day from night, the sun, moon, and stars
- Creation of the sea creatures and birds
- Creation of the land creatures; creation of man
In the first Meditation, Descartes' motivating goal is achieving "anything in the sciences that was stable and likely to last." Certainty is the path to reach that goal. Cutting away anything that could plausibly be denied without a logical contradiction is the negative path to certainty. And because "whatever I have accepted as most true I have acquired from or through the senses," the focus is on doubting exactly that, what he has acquired from or through the senses.
I'm a bit inclined to argue that the senses do not deceive, the mind deceives itself, e.g. you see a figure in the distance and think it is your brother but it is not, or see a bird and think it's a sparrow but it's a swallow. In both cases the senses transmit the image of what is seen and the mind judges what it is, and sometimes gets it wrong - but isn't the fault of the mind, not the senses? But it is true that on account of this sense perception, the mind makes a mistake. Because it is sometimes mistaken, you can plausibly question anything brought to the mind by the senses and dismiss it as non-certain.
The rest of the Meditation is spent answering objections to this idea in a dialectical way. Our sense of personal place seems certain, but we have that sense in dreams, and is it certain, i.e. is it a logical contradiction to assert, that we are not dreaming now? Perhaps not, but the images in dreams, like paintings, are based in reality and hence exist, or if not, the colors used to depict them are real and certain; more abstractly, the universal concepts we have regarding beings is real and certain - bodily nature, extension, shape, quantity, size, number, place, and time. The shape of consciousness is being worked out. These are the categories our minds seem to work in, despite rejecting as authoritative anything coming from the senses. And God made us the way we are, so we can trust categories like these.
But what if God made us wrong and/or continually deceives us out of spite, so that our categories of space-time, place, number, material being, etc. do not correspond to reality but are imaginary? "God wouldn't let us be deceived all the time," is the obvious rejoinder from the faithful, but he lets us be deceived some of the time, and both appear to be equally foreign to his goodness. Choosing atheism leads to the same thing, since by whatever cause I exist so imperfectly in deception and error, so much weaker is that cause, and therefore so much more likely am I to be such a being who is deceived all the time on categories like space, time, place, material being, extension, etc. Thus this Meditation ends not in light, but in darkness.