Win 98 would not load after installing the last patch and playing the game once.

I took the computer to the computer shop I bought it from.
They said the culprit was Civ3 and they fully uninstalled it.

Everything works fine now.

I had installed all three patches.

I never did like the way it messed with the config files and monitor settings every time I played the game.

Not sure what to do now. I enjoyed the game but I need my computer to work.

Try to reinstall the game and apply the newest patch (and just the newest patch). If the problem persists, then I'd say you're out of luck.