Things you need to definitely try before punting and sending the camera to Nikon for repair:
- Make sure you haven't accidentally released the lens. On recent Nikons with the bigger Lens Release button, it's very easy to accidentally partially press this button without noticing, and if you did that while twisting the focus or zoom ring on the camera, the lens may not be set right. Unmount and remount the lens.
- Check the settings! Both the lens and the body may have Focus Mode controls, and if any of them are set to Manual focus, that's what the camera does.
- Check more settings. Did you assign focus to the AF On button (or equivalent)? If so, the camera doesn't focus unless you press the button.
- Inspect and clean the contacts on the lens and camera body. On the lens, the little nubs should spring out on being pressed; none should stay depressed. To clean the contacts, use DeOxit, which should be in your regular cleaning kit.
- Inspect the mirror box, specifically the area underneath the shutter. Because the AF sensors point upwards from the bottom of the box, any hair, dirt, or other large gunk that ends up at the bottom of the mirror box may block the focus sensors.
If you have a D3s and focus disappears in low light at random intervals, welcome to the club. I reported this one to Nikon within days of acquiring a D3s and have a long list of complaints from others that have encountered the same thing. The problem is that it is random, happens rarely, and only seems to happen in extremely low light (often light with strong color cast), and usually only when the subject is relatively low contrast. Thus, it's near impossible to replicate, let alone document. Why only on the D3s? Because it's the only camera we'd ever try shooting at extremely low EV lighting values, values that are near the stated minimum capability of the focus system. The solution is usually simple: shut the camera off and turn it back on. Or you can just wait. After a few minutes the camera usually starts acting fine again, which makes me believe that the problem is an internal loop with a long timeout. But it's annoying when it happens.