UPDATE 5/12/2019: This theory is confirmed by Season 8, episode 5, "Bells".
Fans have been speculating about the conclusion of Daenerys Targaryen’s story since before Game of Thrones existed—and readers of the A Song of Ice and Fire series have often theorized about her descent into violent insanity as a Mad Queen of sorts. It’s not too hard to figure out where these theories sprang from. After all, Daenerys is the daughter of the infamous Mad King Aerys and has already shown a predilection for burning things.
Despite all the Mad Queen predictions, one of the series’ main protagonists becoming its ultimate villain would still qualify as a major twist. It’s also not all that unlikely of an outcome—not if all the cryptic evidence and supposed foreshadowing are to be believed.
Dany's entire campaign was based on the logic that her heritage as the last surviving Targaryen grants her the most rightful—or 'legal', you might say—claim to the throne. Indeed, it's this succession logic she references throughout the series whenever her claim is challenged. So, having proven herself such stickler for the rules of royal lineage—to simply maintain internal consistency, here—Dany is practically required to swallow her own medicine if she ever learns that in fact she does not have the most legitimate claim to the Iron Throne. She made this bed!
Enter Jon Snow. When he reveales his true parentage to Dany, she reacts in horror, and literally begs him to keep it secret. This is not an unreasonable response by any means: after all, Dany has shed a lot of blood, sweat, and tears in her pursuit of the Seven Kingdoms. She's poured an incredible amount of resources into her Westerosi initiative—both personal and capital—and her panicked reaction to Jon's news is totally understandable.
Still, if her entire justification for her pursuit of the crown was that she has the most legitimate claim to it in the entire Game of Thrones world, she should have ultimately conceeded to Jon that he's the one who deserves it. In fact, if she believes in the royal succession she's based her entire campaign on so much, she should have ultimately demanded that Jon Snow take the Iron Throne.
Instead we got an angry, anxious, and bitter Dany who made it clear that she has no interest in abandoning her quest for power. Will she go to extreme lengths in the pursuit of it?
There have been several lines of dialogue thus far in Game of Thrones that could be seen as foreshadowing Daenerys Targaryen’s transformation into a Mad Queen, and many of them come from Daenerys herself. When she’s not committing actual massacres, she can often be found threatening people with fire—like the time she told Varys she’d burn him alive if he ever betrayed her.
Other examples of foreshadowing are more subtle. When Tormund Giantsbane glorifies Jon Snow’s dragonriding, he makes an interesting observation.
What kind of man rides a dragon? A mad man! Or a king!
Jon certainly fits the profile of a king—so does that leave Daenerys as the mad one?
In King Aerys II Targaryen’s final moments—before being skewered by Jaime Lannister—he screams the same thing over and over: “Burn them all!” He’s referring to his enemies and the people of King’s Landing alike, and the phrase has become symbolic of his violent extremism. Now, Daenerys Targaryen might have a pyromania-inspired catchphrase of her own.
Just before she’s executed by Gregor Clegane, Missandei of Naath shouts a final word to Daenerys: “Dracarys.” The Valyrian word roughly translates to “burn,” and it’s usually directed at Dany’s dragons. This time around, however, it could be Daenerys herself that the word incites.
Emilia Clarke obviously isn’t spilling the beans about the conclusion of her character’s story arc, but her interviews haven’t exactly painted a positive picture for the future of Daenerys Targaryen on Game of Thrones. Speaking about filming the series’ final scenes to Vanity Fair, Clarke sounded fairly pessimistic.
It f***ed me up. Knowing that is going to be a lasting flavor in someone’s mouth of what Daenerys is…
George RR Martin himself, the author of the A Song of Ice and Fire series, has also hinted at a less-than-happy ending for his protagonists.
People ask me how Game of Thrones is gonna end, and I’m not gonna tell them … but I always say to expect something bittersweet in the end. You can’t just fulfill a quest and then pretend life is perfect.