Ok, I just wanted to see if anyone was interested in hearing more.
This is almost everything (plot-related) that I've come up with so far. There are some other random details in my notes that aren't too important to the plot, I won't share those.
Alison ends up escaping the government fairly early, although she doesn't realize the true reason for it; she didn't really outsmart the gov, she simply was unaffected by their attempts to stop her. I'll explain that in a few lines.
Alison is on the run. She's not very good at it, since most people don't do petty things like "camping" anymore. Also, the gov't seems to be especially good at finding her. It's almost like magic.
Eventually, Alison ends up in The Cave. I'm not sure if she finds it on her own, or if someone leads her there. The only entrance to The Cave is by swimming down into a pool of water, and the pool is contaminated with iron, so it repells magic. Inside The Cave is a secret hideout for mortals. All of the escaped mortals are trying to stop the government, because the gov't wants to wipe out mortals. Alison joins them.
Why does the gov't want to destroy the mortals? Well, it turns out that the mortals aren't as powerless as they seem. See, they have the power to see through all the mind tricks. The government is officially a democracy, but their hasn't been a presidential election for over a decade. The power-hungry politicians have found a new type of power; Dark Magic. They're using mind control to keep the people under control, but the mortals are immune (at least, the ones that haven't been exterminated are).
Eventually, The Cave gets an unexpected visitor; Alison's (ex-)boyfriend. Alison convinces the rest to trust him, but he can't do much but inform them about the gov't's actions. If he were to fight, the gov't would control him. As it is, if he is caught they could interrogate him for The Cave's location, and he would have to give it to them.