How to build a Reaver-killing reader

I have been in a funk lately, and in an attempt to get out of it, I've been re-watching Firefly in hopes that it will make my brain happy and humming along again. It has definitely got me thinking about the 'verse again. There are so many unexplained loose ends and gaps, and I'd like to speculate about them again!

Burning Question #1: What did the Alliance do to River's brain?

We know a few things for sure:

• They opened her skull and cut into healthy brain tissue "again and again," according to Simon's analysis of River's brain scans


• During one of these sessions, they stripped her amygdala, rendering her unable to suppress her emotional responses


• They also "programmed" her with trigger words to a) get her to fight, apparently with anyone (if not ordered to attack specific targets?) and b) to go to sleep (as a failsafe in case something goes wrong with her)


• They stuck what looks like a big hypodermic needle into her forehead during her last day at in the Academy labs (in the movie)

We also know a few ways she's changed since her pre-Academy days:

• She often seems to speak and/or understand in metaphors - she's like apple bits in reverse, "The sun comes out... / darkness is come again," "They took Christmas away...nothing but coal," Book's hair as too much snow on a roof, etc.



• She might actually see things differently, like the gun that is a branch of cherry blossoms


• She can read minds (she might have been able to do so before, but we have no evidence of this -- she certainly displays this ability more than she did before, anyway)


• She's still capable of understanding things the way others do sometimes, and remembers everything that happens whether she appears to understand at the time or not (eg, she knows what Simon has given up for her and can express this); these lucid periods come and go, and might depend on the time of day (well, the time since she's woken up anyway), if her being lucid in the morning and falling apart later in the day in "War Stories" is not just coincidence


• She really, really doesn't like Blue Sun Corporation

So....what did they do, exactly? And why? ( Curse your sudden but inevitable cancellation! )