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.
Simple answer: don't use manual mode.
What's happening in your situation is that you are using full manual mode but have not taken the care to choose an aperture and shutter speed that would result in a correct exposure, so other than a few happy coincidences where the ambient light level just happens to match whatever aperture and shutter speed the camera was set to on the day, photos are not going to be correctly exposed. Underexpose by more than, say, 7 or 8 stops (say, by going indoors or by night falling) and it'll just look like total darkness.
The long answer to this is to teach you all about aperture and shutter speed and how exposure is calculated.
But the more concise answer, in my opinion, is just to advise you to use auto mode.
I think there's a prevailing attitude among some camera owners that if they're not in manual mode, they're not doing proper photography. Some people seem to believe that professional photographers always shoot in full manual mode, even if they are taking snapshots of their daughter's friend's birthday party, for example.
Neither is true. Manual mode is specifically helpful for when you want to be able to set a particular aperture and shutter speed. If you are not in a specific situation where you want a specific aperture and shutter speed, you don't want manual mode.
When you shoot in full manual mode you are fully responsible for exposing the picture correctly: making it not too light or dark. The camera will not help you at all. If you shoot in manual mode but complain that the picture is too light or too dark, you are putting the cart before the horse: the whole point of manual mode is for when you know how to set the exposure better than the camera would if you let it choose them automatically. Using manual mode should start with knowing what aperture and shutter speed will result in the desired exposure.
Professional photographers venture away from auto mode because they want to achieve a specific effect by using a particular shutter speed or aperture (or both). That is, they understand what effect a particular aperture or shutter speed has on a picture and want to exploit that. It doesn't sound like you're in this position since you expected the camera to get the exposure right.
If you would like to learn more about the effects of aperture and shutter speed, by all means do so. Also check out the Aperture-Priority and Shutter-Priority modes on your camera, as they allow you to have full control over just one of these settings at a time while the other one is adjusted automatically by the camera.