Windows won’t start – Virus?

I have a friends laptop (W98). It won’t boot – it ?sks “?nsert system disk and press enter key to reboot”
So I put in a startup disk and it tells me that it can’t find a valid FAT or FAT32 partition and says that there could be one of 3 reasons.
1.Not partitioned (it was)
2.Using 3rd party partitioning S/W. (not using)
or 3. Could be a virus. I know she didn’t have the def files updated for a while.

Anybody know how to work around this? Is there a way of scanning the now D:\ drive? (as C:\ is now the startup disk image)

I don’t want to have to reformat it so any suggestions would be welcolme.

Cheers

DaddyMan