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Anders, a Mage who has merged with a spirit of Justice, spends most of the game attempting to help other Mages and oppose the Chantry's Circle system, which is used to both teach Mages to use their powers and basically completely control their lives once they're finished with that learning phase. The tension between the Templars, who maintain the Circles, and the Mages, is present throughout the game in various side-quests, and the third act focuses on it exclusively. And in the end, Anders decides upon a desperate course of action: blowing up the city's Chantry, with its high Priestess, who has been one of the main forces keeping the Templars and Mages from coming to blows in the third act, inside of it.
Long story short, this ends in a full-blown war between Mages and Templars erupting not only within the city the game takes place in, but throughout the continent. Which is exactly what Anders had hoped it would do, as he saw no other way to free the Mages of the world from the Chantry's oppression.
Many players actually complained about this, since it left the player unable to resolve the dispute peacefully or prevent the war. Myself, I see it as a high point of the game, and a good sign for Bioware, since you're quite right that other characters acting only on the protagonist's whims is a problem they have in other games.