@Wolvenworks@Tamerlane I'm guessing is that the highest tier magicians/witches are using the lower tiers and commoners for their dangerous experiments/fetishes, and the ex-Major resigned from his position in order to find a way to stop them. The Colonel is in the know but can't do the same, as the upper-tier assholes would put a puppet in charge of that group, which seems to be the magic Special Forces.
@HDMI1 That seems about right. Although I feel like it's more likely the guy resigned for some other reason, maybe intending to just get out of the game or maybe because of some corruption issue, crossed the wrong person or what, and realized later what was going down and felt forced to start doing something about it.
'Feels like all of this drama is a tad forced / out of place, in what is otherwise a pretty wholesome story about an apprentice and a quirky master.
I'm sure that's just me, though.