My idea is that the BMRF, instead of being invaded by the HECU, had its entrances and exits heavily sealed to the point of no return, so the HECU could focus on the surface. After Gordon killed Nilhianth, and was placed in statis, the world returned to normal.
Several generations pass, and the facility has faded from the public eye. Several factions exist inside, growing crops and raising xenians. You are in one of those factions, and a crisis has arisen: the reserve power is running out in your sector. You are sent out to find another source, possibly from one of the neighboring sectors.
As far as I know, an RPG structure can be made in Source.
https://www.gamecareerguide.com/features/1106/diy_rpg_make_your_own_rpg_with_.php