When running Scan Disk in a Thorough mode, the scan always stops at 79745 out of 1054200 clusters. Why won’t the scan complete its task? The computer is running Windows 98.

We should first try running Scan Disk in Windows Safe Mode, in case something is running in the background to cause Scan Disk to stop during its execution. Restart the computer and when the ‘Starting Windows 98′¦’ message appears (just before the Windows 98 logo splash screen) start pressing (tapping) the F8 key. The Windows startup menu should appear. Select ‘Safe Mode’ from the menu and press ENTER. Windows will load into Safe Mode. Then, try running Scan Disk to see whether the program will execute to completion. If so, you will probably need to run Scan Disk in Safe Mode in future occasions. Anyway, I think it is a good idea to run Scan Disk and Disk Defragmenter in Safe Mode, to ensure no background programs or processes will interfere with the operation. Once you are done in Safe Mode, just go to the ‘Start’ menu > ‘Shut Down’ > ‘Restart’ to restart the computer back into Windows normal mode.

Should the problem continue when running Scan Disk in Safe Mode, it is possible that there is an error on the hard drive which is causing the Windows Scan Disk sessions to stall. So, we should try running Scan Disk in real mode (i.e. in DOS mode, from the command prompt). Start Windows back into Normal mode, then go to the ‘Start’ menu > ‘Shut Down’ > ‘Restart in MS-DOS Mode’. Windows should shutdown and load the command prompt. At the prompt, type the following command:
scandisk /surface
This command will start Scan Disk and run a scan of the hard drive. At the conclusion of the preliminary scan, Scan Disk will also perform a surface scan (this is the operation which Scan Disk performs when set to Thorough mode). Should the real mode Scan Disk successfully complete its operations, this may have fixed any errors which could be causing the Windows-mode Scan Disk to hang. So, now try running the Windows-mode Scan Disk to see whether it can successfully complete the scan. To boot back into Windows, either press CTRL-ALT-DEL to restart the computer, or if that does not work, power-down the computer and then turn it back on.

If the problem is not solved, we can try running Scan Disk from a DOS boot disk. Be careful with this procedure, as it is quite technical and may result in data loss (albeit, there is a very low chance of this happening). In any case, you should always have a backup of your important data before undertaking any procedures like this. With the disclaimer out of the way, we will first need to create a startup disk. Before starting, make sure you have a blank floppy disk. Then, go to the ‘Start’ menu > ‘Settings’ > ‘Control Panel’ and open the ‘Add/Remove Programs’ control panel. In the window that appears, click the ‘Startup Disk’ tab and the ‘Create Disk’ button. Follow the wizard to create the startup disk. This disk should already have the Scan Disk program copied, so now we need to boot from the boot disk and run Scan Disk. Put the floppy disk into the drive and restart the computer. The computer should boot from the floppy disk. Once the computer has finished booting off the disk and you are at the command prompt, type the following command:
Scandisk /all /surface
Once the scan has completed, boot back into Windows to see whether the Windows-mode Scan Disk will work correctly. To do this, as previously, either use CTRL-ALT-DEL to restart, or power-down then turn the computer back on.