Depends on which route you want to take the story. If the effects are reversable, then things become relatively striaghtforward. Maybe the evil team made a remedy, or maybe it's a more mystical thing like the Anistar sundail or some legend/legendary.
If the effects are permanent, then the development can be about acceptance. While the evil plans can still get foiled and such, the protagonists could meet other people going through something similar. Maybe those less fortunate who were successfully brainwashed/forced to obey by the team. Maybe they try to settle somewhere remote, like the endgame idea I remember being suggested from the start, or maybe they try to deal with the oddities and reintegrate into society. Families exist, too, and they can play a part in that sort of development.
But, as a reminder, don't make a plot too specific -- make it flexible. A lot of good ideas have died because the plots were made to specific and the others were sorta forced into that or went off course to the point where the creator didn't know what to do.