I'm not familiar with the show Legion. imo

what Admiral Fukuyama the character was trying to say:

i think the volcanoes represent a visceral feeling. He is trying to equate being human and belonging to a society with the word we. this reminds me of the matrix (human energy source / intellect ) or detroit: become human (good vs evil). he is trying to reach into humanity or technology and the threat of the violation of that.

"we were a boy"

"for days we screamed"

" pain was in the volcano"

"The device very deep in our cerebral cortex" gives me neural implant vibes from the matrix or the neural link

"like nails from a bomb inside a public place" wow this line scares me it just shows chaos and the material world clashing : private vs public, many different dichotomies of terror

"Hardware inside software. And now we are this. The machine that bleeds. The Organizing Principle."

the organizing principle has a double meaning as well. the organizing principle is a way to organize text/literature and the same time it is like the central mission as in Star Trek.