First, create a restore point.
You are in the windows\system32 folder.
Switch to the C: drive and try to run it from there.
Or try tapping the F8 key on startup (may be different on some computers) until you get to the screen that has Safe Mode, Safe Mode with networking ,etc. Choose the first option Repair my Computer, the select the command prompt and do a chkdsk from here.
NOTE: You will be in a directory called X:\windows\system32.
If you have a factory partition, you'll need to locate it by changing to the D: or E: drive and do a dir /p to locate the actual C: drive. No change back to the X:\ drive ( at the root and run the command here making sure you're selecting the C: drive or partition