The Ragesians generally don't trust magic users. They have an elite group of people, inquisitors, trained to deal with magic users. When the emperor was killed, Leska needs a good scapegoat, and her people already don't like mages. Plus, getting rid of enemy mages gets rid of the only real threats to her power.
Most of the mages who were living in the Ragesian heartlands were caught off guard. Inquisitors appeared at their houses in the middle of the night, accompanied by copious numbers of soldiers, and the majority of those mages weren't prepared to defend themselves. A few spread the word and escaped before inquisitors got to them, taking along their friends or family members. Many were caught by Ragesian patrols along the border of the empire, but enough got through that, when the PCs get to Lyceum, they'll find a few thousand refugees (though most of them are friends/family, not actual magic-users).
It's like if the American government decided to become a totalitarian state, and sent out the military to round up those people who are suspected to be opposed to the government. A lot of people really aren't much stronger or more dangerous than you or me, and they get taken easily. A few folks who live on survivalist ranches are harder to deal with, but you've got to break a few eggs if you want to make a dystopian dictatorial omelete.
Bear in mind, just because they're magic-users doesn't mean they're inherently stronger than non-mages. If the Ragesians were going to take down a 10th level mage, they sent in an 8th level inquisitor, a few 8th level fighters, and some 8th level rogues.
And if you want to know why Leska is really doing this, tell your players not to read this next piece.
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The case recovered in the first adventure contains schematics for a massive eldritch machine to draw power from the channeled agony of magic users. In the 8th adventure, O Wintry Song of Agony, the heroes will head into the northern wastes of Ragesia to assault the gulag where these mages are being kept, and they'll discover just what strange weapon Leska was constructing.
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Any questions?
