How to set my NikonD5000 properly?

The last time I used my Nikon was 3 days ago, and I think my brother used it and changed the settings. I'm no pro in using this camera, since it's new and I don't know a lot about photography.
I used it earlier, and every time that I will take a picture of something, it won't focus. Both, Manual, Scene or any settings. And all the photos that I took are blurry and dark. I looked at the settings, but nothing changed (For me. 'Cause I don't know much about the settings yet.). Can you help me with this? How can I set it back properly?

In addition to the AF/MF button on your lens, the camera has a two button reset on the top.

Now do yourself a favor. Read the manual and learn what all the buttons do.

And never let anyone else use your camera until you learn what each setting does, and how to change them to what is needed whenever you use it.

This will be a learning curve for you, but that is why you bought a DSLR in the first place, right? Have fun and learn all you can about your camera.

Use the cameras light meter to determine the proper exposure

Shoot at shutter speeds of 1/250th or greater to prevent blur caused by camera or subject movement

NEVER let anyone use your camera

Read the user manual

Here is how to balance the three important factors when picking an exposure; ISO, shutter speed and lens aperture

http://camerasim.com/camera-simulator.html

In front of the camera, to the right side is the AF/MF switch. Put it back to AF (or AF-S).