Summary: Daenerys is already going down the path of becoming a villainous tyrant, and her chapters make up the origin story behind what will become the greatest threat to Westeros. Reasoning: Daenerys' actions have been getting more erratic and less benevolent as the series has progressed. She also has a tendency to bring death and destruction everywhere she goes, from the House of the Undying to the cities of Slavers' bay. Why should Westeros be any different? A related theory is that Daenerys is either in the process of turning, or already is, mad. Targaryens are known for their tendency to veer on the wrong side of sanity, and her father King Aerys II was literally nicknamed the Mad King. It's also interesting to note that we have never seen Daenerys outside of her own POV chapters, and there's no guarantee that she's a wholly reliable narrator of her own actions. Likelihood: As recounted by Barristan Selmy, "King Jaehaerys once told me that madness and greatness were two sides of the same coin. Every time a new Targaryen is born, he said, the gods toss the coin in the air and the world holds its breath to see how it will land." Similarly, this theory seems like it has an even chance of going either way.
