I think he went AWOL on the Enclave, because in Fallout 3 w/Broken Steel (canon material since it's mentioned in New Vegas) you meet Stiggs whom the Enclave picked up from the side of the road half dead in order to work on the robots.
But, why would they need Stiggs if they had Dr. Whitley!? I hope that Dr. Whitley survived and we run into him in Fallout 4 (or whatever the next one is called). It would tie in all the games a little bit better.
If there is a post about this already, please direct me to it, thanks.