My honda civic won't start for whatever reason. It drove fine then all of a sudden one morning it wouldn't turn over. My mechanic doesn't know the reason. Its not the starter, battery, or alternator. Is there some theft prevention built into 2000 honda civics that I don't know about ?

If the Check Engine Light comes on and goes off after 2 seconds, when the ignition switch is turned to ON (Position II), then replace the Ignition Control Module (ICM) and coil:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-selected-other-vehicles-46563-4.html#post265896

These are 2 of the 3 most problematic components on this generation of Honda. I recommend replacing them every 120,000 miles or 10 years, whichever comes first. They are responsible for many Hondas suddenly dying.