I was taking mass photos a few days ago, and I had it set to Manual, when after about four photos, the rest started coming out black. I could see through my eyepiece clearly, it took the photo normally, but when I reviewed it they were all black.
"Manual" means that it is up to you to set the correct exposure. It's conspicuous that you didn't mention what exposure settings you were using, so I'm not sure that you realize that you have to do that yourself.
DSLRs have light meters in the viewfinder which show how over/under-exposed your manual settings are, according to the auto-exposure system. On Nikon cameras it shows up as a bar:
If the meter is in the middle, then the autoexposure system considers the picture correctly exposed. If the meter is to the left, it is overexposed, and to the right, it is underexposed.
Of course, there's no point in using manual if you blindly follow the autoexposure system's recommendations. But if the meter shows severe underexposure, then you're probably underexposing the image and will get a black image.
Increase the aperture or decrease the shutter speed, or switch to an automatic mode (such as P, S, or A).
The obvious answer is that you're underexposing them. What shutter speed, aperture, and ISO were you using? It sounds like maybe the first few were with a setting that was correct, and then perhaps a dial was moved. The effect of this won't be visually previewed in the viewfinder, although the viewfinder status numbers will tell you how the camera is set.
In manual mode, it's your job to set these so the exposure is right. If you use a combination which records too little light, you'll get a very dark or even all black result.
These three factors have to all be correct in concert: if all three are low, you'll need a lot of light. In medium light, you can leave two factors low and set the other higher, or you could increase all three slightly. For example, if you're indoors at night, setting your camera to ISO 100, aperture at f/16, and shutter at ¹⁄₂₅₀th of a second will give you a dark image, even if you can see just fine with your eyes. You could leave ISO and aperture the same and raise the shutter to about 8 seconds, but unless you're shooting still subjects and your camera is on a tripod, that's probably not an option. Instead, find the optimal combination of all three factors which causes your scene to be exposed correctly.
When in complete doubt, try putting the camera back to an automatic/program mode and reviewing what settings it selects.
It may be worth adding that you don't have to use manual exposure in order to get manual focus — these are separate systems.