Perhaps at Aperture they used teleportation tech to capture and use an advisor as a weapon, creating a superadvisor. Then the advisor broke free of control, crashed the borealis, and projected himself as the gman and used his super advisor powers to bend time and cause the events of half life...
Okay, I have thought long and hard about who the Gman is based on what we have been given in the storyline, and I have come to a conlusion that I think is not only a great explanation but also would make an awesome episode 3...
SPOILERS
The Gman is an advisor. Bear with me...