That reveal is one of the smaller "mysteries" that I want to know more about. What exactly happened "a year and a half" ago, if anything, to make her realize it? As for the larger mystery of what the Colony is, I'll put my tin foil hat on and say the leader is Jacob Kane. Or even Kate herself, somehow. To be clear, both of those would be really horrible ideas, but I'm mentioning it now just in case that's how it turns out.