Assuming you have the Gateway recovery CD, you can choose to do a full wipe and reinstall. Don't simply do a reinstall of Windows, because it's a house of cards, as a friend of mine found out while trying to reinstall his AV (Norton).
Start off with a fresh install of Windows, get a firewall and an AV, don't start adding a lot of programs he might not ever use, and I predict it'll be good enough.
Contrary to what some say, '98 is far from dead or useless.
You do know that Microsoft no longer provides either support or updates for 98, don't you?