[@dreamingflowers]
HQ is underground and part of the sewer system. You know how there's [url=http://www.sewerhistory.org/grfx/wh_region/canada_mc/images/01-aerial-tributary.jpg]tunnels that has the actual poo-water running through[/url] and then there's [url=http://vignette3.wikia.nocookie.net/fallout/images/c/c8/Sewer_storage_room.jpg/revision/latest?cb=20131021231923&path-prefix=es]maintanence rooms[/url] and stuff... HQ will be a series of these rooms, I guess.

It would be best if "we" were all working together against the "Big Bad" for sure and anyone who is not yet part of the Resistance will certainly get the oppotunity to become part of it, but is your (character's?) choice if they want to or not. It'd probably be more fun to at least work with the Resistance and eventually join the "quest" to find and dethrone the Technopath...

.:EDIT:.
I imagine the HQ being somewhat like Ninja Turtles' sewer home, actually xD