Hi William
I'm guessing that it's not just that your 'home page' which opens with a new window, or when Safari starts, is wrong ? (if it is that, you can alter it in Safari - Preferences - General)
It sounds like some sort of add-on or extension has changed Safari (a screenshot would help, if you can)
Extensions can be disabled/selected in Safari - Preferences - Extensions
other add-ons can be in the folders listed at http://support.apple.com/kb/ts3230
If it's not an extension, and you can't find any other add-on - please post a screenshot if possible, and also test briefly in a New User Account, since that will tell us where to look