Dragons are one of the most important parts of Game of Thrones, but by the time the HBO fantasy series begins, the creatures have already been gone for generations. When Daenerys Targaryen receives three dragon eggs in Season 1, they are considered little more than ancient curiosities, and even Viserys Targaryen speaks of dragons as creatures that died long before he was born. Daenerys eventually changes things by hatching Drogon, Rhaegal, and Viserion, but their return raises an obvious question: how did they go extinct in the first place?
The answer is more complicated than the Dance of the Dragons. The Targaryen civil war destroyed most of the remaining dragons in Westeros, but the species was already in decline. By the time the final dragon died during the reign of Aegon III Targaryen, the once-mighty creatures had been reduced to a handful of sickly survivors.
Long before the Targaryens conquered Westeros, dragons were closely associated with the Valyrian Freehold. The Valyrians had learned how to tame and ride dragons, eventually using them to build one of the most powerful civilizations in the known world. But approximately 400 years before the events of Game of Thrones, that civilization was destroyed when the Doom of Valyria struck. The large-scale disaster killed enormous numbers of people and dragons, leaving the Targaryens as the last surviving Valyrian dragonlords with living dragons.
The Doom of Valyria took place in 102 BC, while Aegon's Conquest happened 100 years later in 2 BC.
Aenar Targaryen had already moved his family to Dragonstone before the Doom and taken five dragons with him. If he hadn't made this choice, the Targaryens could've been wiped out entirely. Later, Aegon the Conqueror used Balerion – along with his sister/wives Visenya and Rhaenys, and their dragons, Vhagar and Meraxes, respectively – to conquer Westeros. The Targaryens then became the keepers of a dwindling species, but even though they kept breeding dragons, the creatures that were born were not nearly as powerful.
One of the reasons these dragons were less powerful might be that the Targaryens didn't give the creatures sufficient freedom. The construction of the Dragonpit in King's Landing restricted their movement and slowed their growth. Of course, the decline wasn't immediate; there were still around 20 living dragons by the end of King Viserys I Targaryen's reign, but the following war had detrimental impacts.
As House of the Dragon fans know, the Dance of the Dragons was supposed to decide who would inherit the Iron Throne after Viserys I's death, but instead, it nearly destroyed the Targaryen dynasty. Both sides of the conflict possessed dragons, meaning the civil war became a war in which the most powerful creatures in Westeros were turned against one another. Dragons killed dragons in battles across the realm, while others died alongside their riders.
Vhagar, Caraxes, Meleys, Vermithor, Sunfyre, Dreamfyre, and numerous other dragons died in the conflict.
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