I bought into the idealism of the Railroad in their mission to protect self-aware sentient beings. So I was totally sympathetic to Paladin Danse's
The BoS really annoyed me with its negative attitude to Danse and capped that off by telling me that I had to help them take out the Railroad, so biting the bullet and alienating them by doing the Mass Fusion thing for the Institute seemed like a no-brainer.
I went on a rampage, killing everyone on board the Prydwen and wiping out the BoS remnants at Cambridge Police Station. Naively, I figured that the Railroad would appreciate me springing to their defense.
What I didn't realize is that my Railroad "friends" somehow listened in while I was being told to take them out and assumed that I would comply with the wishes of the BoS. I, on the other hand, assumed they'd still be my friends, until I got back to Red Rocket where I had parked all my accumulated companions and the Railroad guy Deacon went ape**** and tried to kill me.
It was dark, I didn't know who was shooting, and it turned into chaos with allies getting wounded, resulting in a few cycles of reloading to get past what I thought was some sort of glitch or bug.
Finally, I accepted the inevitable. Deacon was never going to give up. Deacon had to die. With a heavy heart, I laid him to rest in a pile of green goo and collected his belongings to give them to his next of kin under the old North Church.
Sadly, my dear friends there treated me very inhospitably. Reasoning with them wasn't an option. It was noisy. It was messy. However, I did enjoy wearing Tinker Tom's headgear for some time afterward as a mark of respect to his generosity in teaching me about Ballistic Weave and for the Weathervane Missions.
Gone were my aspirations of a relatively cooperative, inclusive and peaceful Commonwealth.
Sole Survivor 2.0 may fare better.
I have to say I'm not overly pleased with the way things turned out. I got lectured by various companions which made me feel even less pleased. However, the laws of unintended consequences are a part of real relationships with our broader environment, so hoping for "and everyone lived happily ever after" was unrealistic. I get that now.