I know this is kind of the long answer but its pretty insightful.
Windows 2000 includes two repair choices Manual Repair and Fast Repair. To use the Emergency Repair process:
Boot from the W2K installation disks or install CD and you will get an option to repair or install.
Press R to signal you want to repair and existing W2K installation
Press R again to use the Emergency Repair process. When you do this, you see the two repair options:
Manual Repair: To choose from a list of repair options, press M.
Fast Repair: To perform all repair options, press F.
There is a major GOTCHA! with the repair options: Don't run these recovery options on a domain controller unless you have backed up the Active directory database. Running either of these recovery options on a Windows 2000 Server domain controller, you can overwrite the Active directory database, \WINNT\NTDS\ntds.dit. See my tip on ntds.dit for more information on the Active directory data store. To restore Active Directory, you must reboot the system in directory services restore mode, a form of safe mode that ensures that the system is in the proper state to have its AD database overwritten. The special recovery issues of the AD db do not apply to member servers and workstations.
Manual Repair
If you chose the manual Repair option, select the repair option by using the arrow keys. Use Enter to select or clear each check box. The Manual Repair option does not give you a choice to repair the Windows 2000 registry files. The Manual Repair option provides the following choices:
[X] Inspect startup environment
Checks the ARC path in the boot.ini file for a path to the Windows 2000 boot partition and %SystemRoot% folder. If the Boot.ini file is missing, a new one is created with a valid ARC path. If the Boot.ini file is present, the ARC path is checked and updated if needed (it uses setup.log created by the ERD to do this). Basically, this manual repair checks the files used to boot ( boot.ini, ntldr, ...)
[X] Verify Windows 2000 system files
Verifies that each file in the Windows 2000 system/boot partition is good and matches the files that were originally installed. This includes the Ntldr, Ntdetect.com, Arcsetup.exe, and Arcldr.exe files that are used for booting various computers. The optional Ntbootdd.sys file is never checked. Repair performs this check by using the Setup.log file to compare cyclical redundancy check (CRC) values for each file. If files are missing or corrupted, you are prompted to replace or skip the file. If you choose to replace the file, you need the Windows 2000 installation CD-ROM or an OEM driver disk that contains the correct file(s).
[X] Inspect Boot Sector
Checks the MBR and fixes any problems. It will not remove MBR viruses.
Repairs the active system partition boot sector and reinstalls the boot loader functionality. If the partition uses the FAT or FAT32 file system and contains a non-Windows 2000 boot sector, this repair option also creates a new Bootsect.dos file to be used to dual-boot MS-DOS, Microsoft Windows 95, or Microsoft Windows 98 if these operating systems were previously available to be booted. If you also select the Inspect Startup Environment option and a new Bootsect.dos file is created, Repair adds the following entry to the Boot.ini file: C:\ = "Microsoft Windows"
Fast Repair
The Fast Repair option performs all the repairs available in the Manual Repair option, but you are not prompted for choices. Additionally the Fast Repair option tries to load each Windows 2000 registry file (SAM, SECURITY, SYSTEM, and SOFTWARE). If a registry file is damaged or cannot be loaded, Repair copies the missing or corrupted registry file from the %SystemRoot%\Repair folder to the %SystemRoot%\System32\Config folder. This brings up another gotcha!
Fast Repair repairs registry problems by using a backup copy of the system registry that was created when Windows 2000 was installed. Using this option may result in the loss of settings and preferences created since that installation. If this occurs, you need to restore your last system state backup or manually copy a more recent version of the registry files from the %SystemRoot%\Repair\Regback folder to the %SystemRoot%\System32\Config folder by using Recovery Console. The files that are located in the Regback folder are from the last time you created an Emergency Repair Disk and choose the option to also back up the registry files to the repair folder.
Both the Manual Repair and Fast Repair options start by performing a system/boot partition file system check. If file system problems are detected and corrected during this portion of the Repair process, you may need to restart your computer and start another Repair process before the actual repair operations take place.
Neither of the repair options replaces the %SystemRoot%\System32\Config.nt or Autoexec.nt files. Although these files are located on the Emergency Repair Disk, they are not checked or replaced during any Repair operations.
