Myria from Breath of Fire 3. The main character is Ryu, a dragon who's entire race was killed by Myria. The entire game is escaping her minions, rediscovering Ryu's past, traveling a vast ocean, and finally a giant desert. When you finally reach her, Myria claims that she is protecting the world by keeping the brood isolated, one of which was Teepo, Ryu's friend from his childhood. Teepo's mind was warped thanks Myria, now believing that he was a danger to himself and others, but Ryu and his party kill him and relieve Teepo of his pain.
When you finally have the final showdown with her, you want to believe in her reasoning of protecting humans, but killing off an entire race of the main character is just awful. The fight itself was as hard as it was epic, by far the longest battle in the game (And it should be since Myria is the final boss).