Didnt they already explain that in the previous chapters?Unmentioned detail: Timothy's order to step up the finding/killing of suspected witches are because he believes his father's behavior is a result of witches doing something to him. Obviously enough, not all the people executed are really witches.
Fairly important spoiler about that - However his father is still alive (for now), in an underground cell in Hermes (The capitol of the church). A fanatic was made to be a fake king got sent back in his place, ordered the succession games, and eventually killed himself. All to guarantee civil war in the world's strongest nation.