The Canon Err 99 is essentially their version of the Blue Screen of Death and simply rebooting may not fix it, but simply cleaning the contacts and rebooting is pretty much all you can do. It's their "unknown cause" error. To quote from the Canon Europe website description of the 99 error code:

This is a general error that can occur because of several different reasons.

The basic troubleshooting steps you can follow are:

1. Turn the camera off and detach everything from the body that can be connected to it: card, lens, and or flash, to eliminate the possibility of the error being on the card, the lens, or the flash. :) You can use the body cap that came with the camera to protect the body from dust.

2. Remove the battery.

   2a. If you have an older model body with a separate clock battery, remove that, too. (60D and later XXD, and 450D and XXXD models don't have one).

3. Clean the contacts on the camera body (many pointers on how to do this on the Canon website).

4. Leave the batteries out for an hour to overnight, to dissipate any residual charge, or alternatively, turn the camera on, or press the shutter button. (See: the How to "reboot" your camera sticky on the POTN board).

5. Replace the battery (or batteries), turn the camera on, and see what happens.

6. If the camera is fine at that point, then add back your card, and test again. Then add back your lens and test again. Then add back your flash and test again. If the error occurs, you have at least isolated it to the probable cause: body, lens, card, or flash.

Sometimes you can't fix it. Sometimes, the camera really is broken and requires service. When I got an Err 99 on my old Rebel XT, none of this (or replacing the clock battery) worked; the power board had shorted and needed to be replaced. Sometimes, them's the breaks.