Daenerys Targaryen's story is one of the difficult lines between selfishness and selflessness, liberation and enslavement, kindness and cruelty. She is the "mother of dragons" and the "daughter of death": feminine, caring and protective, but also destructive, willing to burn the world to the ground to take what is owed to her.
She is also a character who (at least initially) sees herself as purely good. She is the rightful heir to the throne of Westeros and the protector of her people. She will use her strength, and her dragons, to liberate both literal slaves in the East and the people forced to live under the Usurper's rule in the West, and she arguably would (and does) make a good queen. She agonizes over decisions that would harm any of her people, even if they seem to be for the greater good, and she fiercely opposes slavery and injustice. She is willing to sacrifice her happiness for the good of her people, and she is very intelligent, using her femininity to trick her enemies into underestimating her and then manipulating or destroying them when they drop their guard.
But "destroy" is always the key word in Daenerys' story, whether she recognizes it or not. In order to become a conqueror and take back her throne, Daenerys must kill many innocent people, destroy many more lives, and, as she says, rain "fire and blood" down on the world. She does not flinch from this reality. In fact, she embraces it, and her greatest character flaw is the fact that she cannot see, as others see, that many of her "children" will not welcome this destruction. She still sees herself as the kind and caring mother, without noticing that a mother of dragons must, inevitably, also be the mother of death.
This post contains major spoilers through to the end of A Dance with Dragons.
Daenerys's plotline in A Game of Thrones is so gratifying that it is easy to miss her increasing ruthlessness and brutality. She grows from a meek, scared girl who wants to go home into a determined young queen (or Khaleesi) who will fight to regain her throne, while still feeling kindness and generosity towards anyone less powerful than herself. Far from reviling those who have not yet escaped from the life she once led, she places herself as a protector -- a liberator of slaves, a saviour of women, and mother to all.
Yet she does this by bringing dragons back into the world, creatures of fire and horror and death. Moreover, she does this by burning a woman alive. This woman killed her baby, yes, but she did so to prevent the death and destruction that this child was prophesied to bring to the world, and in revenge for the way that Dany's people already destroyed everything she loved. It is debatable whether or not Daenerys was justified in her execution of the witch, but the fact that she does such a ruthless thing, without any flinch or hesitation, with the desire to hear her enemies scream, suggests that she is already becoming a little bit mad, lost in the fire and the desperation for power. The power to protect and to survive, rather than the power to destroy, yet only death can pay for life, and her fight inevitable leads to destruction for others. In this moment, she is magnificent, but she also hints at the downward spiral that her fight for power will cause.
And so she continued. She arranges a massacre at Astapor, before capturing Yunkai and then besieging Meereen. Perhaps because of her fearful, powerless childhood, she does it all while proudly declaring that she is the blood of the dragon, meaning that she is strong, powerful, fierce and a force to be reckoned with. It is not until one of her dragons kills a six year old girl that she realizes that dragons are, ultimately, monsters. That her relatives have been, for the most part, brutal and insane, obsessed with power and with fire, and that she too may well be the same. That to be a conqueror, to regain her right, and to be Mother to some people, she must be a monster to others.
Yet she cannot stop now -- she cannot look back -- or everything will fall apart. She has blended selfishness with selflessness, the desire to take back the kingdom that belongs to her and to protect the people she has adopted with the desire to liberate slaves and bring peace to a land she does not fully understand. The result is a mess she could not have foreseen, because she did not look beyond what was "just" and "right" to the reality of such rule.
And so, at the end of A Dance with Dragons, Daenerys tames Drogon and flies away from Meereen on his back. Her attempts to return to Meereen fail, and she is found by Khal Jhaqo -- one of her first enemies -- standing beside her dragon, eating the burnt flesh of a Dothraki horse. In that moment, she has become one of the dragons -- wild and fierce and fearless. Remember who you are, she tells herself. Remember the words. She is, perhaps, mad. But she has also finally accepted who she really is, who the Targaryens really are, and who she must be if she will take back her homeland with the power of dragons. She sees what fire and blood really means, and she is willing to take that cost.
Daenerys, for all her goodness, cannot return to being the little girl who longs for a house with a red door. She has travelled too far. Her story is not, as we might originally think, the straightforward and gratifying tale of a powerless pawn of a girl becoming powerful after all. It is also a story of the cost of power, of the dangers of ruling, and of the need for some brutality to succeed.