Casefile: Dr Proton
Lon Matero has written a very cool article which investigates what really happened to Dr. Proton after his battle with Duke Nukem in 1991's Duke Nukem 1. As you may or may not know, Dr. Proton will be returning in Duke Nukem Forever, after his apparent death back in Duke Nukem 1. The article contains background information and many pictures to illustrate the incidents around Dr. Proton's apparent death, as well as an interview with Duke Nukem about the incident, and three theories as to what really may have happened to Dr. Proton.
Please note however, that this article wasn't written by 3D Realms, so it may not be totally accurate insofar as what happened with Proton. As with the X-Files, the truth is out there somewhere. :)