The Scorching Theory 
Contents 1. Dragons 2. The beginning of the Scorching 3. A Dragon-Human War 4. 3 Moons 5. The loss 6. Evolution of dragons
Dragons I like to think that dragons were created by humans as a weapon for war. This explains their warlike behavior. They were created with these things in mind: They were created by cloning factory's. (Kind of like Jurassic park) they used them as a weapon of war. They were brutal but smart. Not as smart as humans though. They weren't like dragons very much, they were more like dog - lizards. The humans made them very adaptable. The humans basically controlled them. The beginning of the Scorching
(Before they created the dragons.) I think that a massive nuke was sent to a enemy country. But it got shot down in space and flew of somewhere far far away. Years later it collided with an meteor and blew up next to a few moons. The explosion made the moons go off course, and some of them went straight toward earth. Finally the moons reached earth, this caused flooding and tsunamis. Meteors and stuff fell from the sky, kind of like the extinction of the dinosaurs. The gears for the dragons screwed up and the they malfunctioned.
Humans vs dragons The dragons were going out of control and killed any thing that moved. The dragons were adapting to the conditions and got smarter and smarter. The humans couldn't stop them and were out numbered by share size of the dragons. Half the population of dragons was destroyed. And most of the population of human was destroyed. Time passed and the details were forgotten.
3 Moons So where do the 3 moons tie into this? When the Moons came to earth, the our moon was obliterated, The three moons would create huge tides, flooding most of the planet. I think this is why there is only one main continent on the planet. But there could be other forgotten islands somewhere. There would also be a huge ocean. Because water is in space, and there would be loads of it in the moon. But the scorching would of taken years to process.
The loss After the loss of the Scorching, the humans lost a lot of their advanced technology. In the generations after the Scorching, technology just became fantasies or myths, like dragons were before they were created. This probably also happened with dragons, too. In Moon Rising, Webs was talking about the Scorching and how there are many different versions of the war being told. Webs said something about how some things about the Scorching seemed fake or illogical or something like that. This could be because humans had advanced weapons like guns, but they now do not.
Evolution of dragons There's a problem: how did dragons evolve and adapt so quickly in about 5000 years? I think humans made the dragons grow quickly and adapt to their surroundings over a short amount of time. Because of the rising tide, the dragons grew wings over the years. The apocalypse came and went. The dragons made there own language and tribes and found and inhabited it.
Thoughts I think in the story now, humans are showing signs of their ancestors behaviour, and will soon create technology again in the next hundred years.