Then you'll have to force the phone into recovery mode and restore it. Turn your phone off:
Then, leave the USB cable connected to your computer, but NOT your phone, iTunes running, press & hold the home button while connecting the USB cable to your dock connector, continue holding the home button until you see “Connect to iTunes” on the screen. You may now release the home button. iTunes should now display that it has detected your phone in recovery mode, if not quit and reopen iTunes. If you still don’t see the recovery message repeat these steps again. iTunes will give you the option to restore from a backup or set up as new.