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She is the only surviving child of King Aerys II Targaryen, who was ousted from the Iron Throne during Robert's Rebellion. Daenerys' mother was sent to safety on Dragonstone island just before the Sack of King's Landing, and died giving birth to her during a great storm which wrecked the remaining Targaryen fleet at anchor, earning her the sobriquet Daenerys Stormborn. She lives in exile in the East.

Daenerys was sold into marriage to the Dothraki Khal Drogo, but lost her husband and unborn son to the manipulations of the vengeful maegi Mirri Maz Duur. Her marriage to Drogo and subsequent interaction with the Dothraki people gives her the confidence and strength to lead and the belief in herself as the rightful queen of the Seven Kingdoms. Following the death of her brother Viserys, Daenerys was left as the last Targaryen, and intends to claim the Iron Throne as her birthright. She formally styles herself as Daenerys of House Targaryen, First of Her Name.

During her campaign in Slaver's Bay, she is introduced as Daenerys Stormborm of House Targaryen, Queen of the Andals and the First Men, Khaleesi of the Great Grass Sea, Breaker of Chains, and Mother of Dragons.

She hatched three dragons by having her petrified dragon eggs placed on Drogo's funeral pyre, before she walked into the flames to claim them. Her dragons are the first seen in the world for hundreds of years, earning her the sobriquet Mother of Dragons.