Did you play the DLCs? Witch Hunt to be more specific?
Spoiler Alert, click show to read:While Morrigan's motives might seem very sinister near the end of the game, but later on, in the DLC and in Dragon Age 2 (don't get that one...it's a turd), it is revealed that Flemeth is actually planning to do something a lot worse and on a far larger scale...probably a story that will arc through the entire series of Dragon Age games, and Morrigan is merely trying to get ready to do something to counter her.
Anyway, she allows the Warden to come with her to meet his son at the end of the DLC so most probably her plans won't turn out to be all that evil...or at least the lesser evil.
The horizon is nothing save the limit of our sight.
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