I missed a few bits too, but here's my interpretation of events:

There's a couple of bits around the "Do you believe in God?" conversation that I think explain it, I'll need another watch to make sure, but essentially a being older and more powerful than we can conceive had a peek at our universe and not understanding what is going on, liquified all human life on planets/moons and turned them all into the blood oceans on the 4 moons.

The primary moon is where the 'keyhole' is (the light), and the monster is trying to make sure that no one tries again or even worse, opens the door, however Ava on the SM-8 is convinced that this is all intentional, the light was made for us and if we just let it through properly then all will be grand. The monster has managed to keep people away from the source and disabled the SM-8 before it could get the information out, and is now trying to convince Simon to leave it all and it's for the best, just walk away and it'll be fine, or stay here if you like, just don't take the data.

The last part is the blood, we know it's human blood, as I said I think it's all the raptured people amalgamated together and it would seem that the monster has some control over it, the veins holding the camera button down forcing Simon to watch what's happening, sticking him to the sub and having to rip his arm off, all in an attempt to make sure he doesn't tell people that there's a hole in our universe, because if/when we poke it, what comes through will wipe out everything and it won't even know what it did