Things were progressing well - I had secured control over starting Island, Fleatown, and Camp la Barriere, managed to build a sizable militia there, including elite members.
My plans to advance Pantagruel were disrupted when Biff from MERC sent out a distress call. I responded, succeeding in saving him (which costed most of my ammo and resources). Then I went to confront Santiago at the refugee camp. I found all its inhabitants - including a few quest characters I had previously rescued but not yet visited - dead. I was accused and ordered to be eliminated and using pretty much all of my stuff I stood my ground (with no casualties, yay!)
However, in the aftermath of the camp incident, while I was licking wounds, about five assault groups seized ALL MY HARD-WON territories.
I'm wondering if I inadvertently triggered a high-level questline? I did make a short visit to the east island (sanatorium), just before Biff's plea for help.
I'm curious to know if any of you experienced something similar - is this just part of the game's challenge?