1. Operating System. Windows 98 Original or Second Edition?
2. The Plan. You should be able to boot to "Command Prompt" from startup menu. Then you can and should verify the integrity of the file system. You can also reload an older version of the registry (one dated before your problems occured). You should be able to recover from this problem. If you are able to successfully boot into Windows (safe mode), I would recommend you defrag the file system since it probably hasn't been done in a while.
3. Startup Menu. Hold down the F8 function key (or tap it about once per second or faster) as you power on the system.
If F8 doesn't work for you, restart your computer and hold down the CTRL key during the Power On Self Test (POST). Holding down CTRL may interfere with some POST chores, such as setting up the keyboard or initializing a SCSI controller. If this happens just release CTRL until the POST resumes, and then hold it down again.
Once the POST is complete, the Startup menu should appear:
Microsoft Windows 98 Startup Menu
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1. Normal
2. Logged (\BOOTLOG.TXT)
3. Safe mode
4. Step-by-step confirmation
5. Command prompt only
6. Safe mode command prompt only
7. Previous version of MS-DOS
Select the "Command prompt only" option and hit "Enter".
4. Scandisk. At a command prompt enter "scandisk /all" and hit "Enter". It will scan and attempt to correct the file system integrity on "all" of your hard disk drives. This will frequently fix many "startup" problems.
You can try to restart your Windows 98 system in "normal" or "safe mode" or you can continue to checking and possibly restoring the Windows registry to an older version.
5. Scanreg. At a command prompt enter "scanreg" and hit "Enter". It will check the Windows registry for corruption and load a backup version if problems found. If registry scans Ok, you have option to view backups. You can "View" the backups and select backup with date before your problems began. If you then select the "Restore" option this will rollback your registry to that date.
By default, your system saves the last "five" backup copies of the registry. It automatically makes a backup every day the computer is on.
Other useful variations of the "scanreg" command are:
> scanreg /opt
> scanreg /fix
Google them for details.
6. Defrag File System. Boot into Windows Safe Mode. Left click "Start", left click "Run", enter "defrag /all", hit enter. Sit back and watch the "cluster" movements.