That's a normal prompt for a chkdsk.
You type y and press enter then restart where the chkdsk will execute.
When the chkdsk has completed, go Start - type eventvwr and press enter when Event Viewer comes up.
When Event Viewer opens ensure Event Viewer (Local) is highlighted - if it isn't then just click on it.
Expand Windows Logs - click on Application - Action - Find then type chkdsk into the Find box and press enter.
Cancel the Find box to read the log in the pane below.
Primarily you are looking to see if it reports any KBs in bad sectors.
If it does then perform a chkdsk /r and when that has completed, create a system image onto external media and a System Repair disk in preparation for a full HDD failure.
After you have performed the chkdsk, try Windows Repair again to see if it completes successfully and reboot.
I normally create a system image before running WR.
If the sfc /scannow still reports that it cannot repair files, then boot up with the USB and follow the steps to perform those cmds I've posted.