If we take everything's that's already happened at Milliways -- including, most importantly, the trip to Taos -- as having happened, there has to be a damn good reason for Charles to end up in the Academy. Charles provides plenty
of canonical basis for getting into dangerous situations because he thinks he can handle them, though.
After his visit to Taos, Charles starts investigating the Academy, and eventually contacts Dewey again to discuss a "trial run." The experiments they're running (see the first half of this
fic) interest him, and he's certain he can get out if things start getting bad.
Of course, by the time things start getting bad, they're so bad that he can't get out. The Academy won't let him simply walk out in the state he's in, and he can't tesser out -- tessering requires knowing where you are, and where you're going, and the drugs have screwed up his brain chemistry to the point where he's almost perpetually disoriented (the planet is tilting too far).
The first six months of his stay at the Academy are more or less described in the above fic. The people running the Academy want to maximize his psychic potential; they want to use him to listen to people, to the world, to the universe, to the stars. People, though, are a lot
louder than most of the universe, and certainly louder than all the stars except the Sun. They've also done some research on him in a purely physical sense, trying to determine what makes him different from other humans. Mostly this has been imaging, not surgery, though there might have been a brain biopsy or so in there.
After six months, Dewey was removed from the project because he was becoming more and more vocal about how terrible it is. Shortly afterwards, Charles was moved out of the Academy to another facility -- or maybe the Academy simply came under new management, as it were. It doesn't make much difference.
Charles doesn't spend so much time listening anymore -- at least, not in sessions. Those mental blocks have been taken down; the chances of them going back up again are slim. But that's not his work anymore.
The Academy gives him problems involving fifth-dimension physics to solve, and tells him that they're "largely theoretical." Of course, it's kind of useless to lie to a psychic. In an ordinary human, even a very good mental block will have chinks. The first few times they tried to get him to solve these "theoretical" problems, though, he panicked. They eventually decided that memories of a number of impossible things -- the Mrs. W's, going Within, the farandolae's Deepening -- were pointing his moral compass in a direction they didn't want.
What followed was an extremely unpleasant few months in which most of Charles' memories of pre-Academy life were suppressed or explained away. There may have been surgical modification at this point -- certainly his hair is a lot shorter now, as if it's been shaved off and has been regrowing.
The two phases of the Academy have used a number of different drugs to get his mind into the shape they wanted. (I don't want to think
about what they've done to the poor guy's liver, not to mention the rest of his body.) There's also the distinct possibility that they're testing new substances on him.
~Alprazolam (for sedation, when things get overwhelming)
~Acetylcholine (a neuromodulater that affects how information is passed between neurons)
~LSD (The US Gov't's favorite "What does this do to the brain?" drug)
~Several experiments with traditional mind-alterers like mescaline
~Caffeine (old-fashioned make-the-brain work faster drug, in concentrated doses)
~Methaqualone (for sedation; stronger than what Phase 1 used because he's built up a tolerance, not to mention that his own inner conflict creates higher levels of anxiety and more freak-outs)
~Further experimentation with neuromodulaters
Charles can seem coherent on some of these drugs, especially the neuromodulators and stimulants -- they mimic, to varying degrees, the mental blocks he would put up for himself. Just because he sounds
coherent doesn't mean he's operating on the same level everyone else is, though (I wouldn't want to listen to his head when he's medicated). Furthermore, those states of mind are when he's least himself and most the Academy's.
When the drugs wear off, he's much closer to the same world as everyone else -- but then his psychic blocks are down, and he has to deal with the sensory overload that comes with that.
*eyes that last bit* I may be going over the top and making him unplayable with all this. Maybe I'll just handwave "He's on drugs! He's 'sane' when he's drugged up and River-ish when he's not" and forget about science. Works okay for Joss.