Hello austin, and welcome to the forums.
You've certainly described what sounds like either a penalty or a bad bug in Google's data. Discovering what might be causing a penalty can be a challenge, but there are other threads here where people are struggling with something similar. The investigation you need to make is very similar, even if you discover something different.
These two tools can help you - the Hot Topics area [webmasterworld.com], which is always pinned to the top of this forum's index page, and our Site Search [webmasterworld.com].
If you are certain that you have not been involved with selling or buying links (Google will often penalize if they suspect that) then the first Hot Topics I suggest you should check are:
1. Hacked Servers [webmasterworld.com] - pay special attention to the new breed of hacker who puts links on your pages that only googlebot sees, not the regular browser. Hackers may also corrupt your .htaccess file or your robots.txt file, so be sure to check those.
2. What type of penalty do I have [webmasterworld.com]
Also, I'd suggest you use a Google Webmaster Tools account. Sometimes the feedback you get there can be helpful.