
Laiho Vanallo |

Creatures from outer space are kidnapping them and performing vivisection on them, replacing their organs with mechanical parts in the goal of using them a cannon fodder in an intergalactic war. Report are of dragon being snatched mid air by strange beams of lights, being carried away in mysterious dark clouds floating high up in the sky at night. Being one of the most fearsome predator on the planet the alien think they they would be perfect to be weaponized.
Imagine the dragon meeting up and talking about their friend being attacked by a powerful unknown (non magical) force and that there is nothing they could do!
The alien quickly learn of the chromatic dragon lust for gold and set up obvious trap by stockpiling large quantity of gold in open fields, a bit like we do with rat traps.

Bob of Westgate |
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Maybe the dragons fled this part of the world ages ago and are returning now because a bigger threat has been created in the part of the world they fled to. Namely gunpowder. When when are the top of the food chain because you have armor almost no sword can pierce and then a horde of gunslingers suddenly start popping up that can cut through you like soft cheese(dragon touch ac sucks) it's time to go. It's the classic technology overpowering magic. And a great way to introduce firearms into a campaign

tsuruki |

God's.
God's are allways threatening.
Perhaps reduce the scope so that not EVERY dragon has to rub from it.
For example:
The dragons. Being masters of their faraway real recreate the world (Or just settle a typical yet fantastical temperate world).
They awaken great old dragon gods and praise them. But eventually Tiamat becomes enraged and sends the dragons a curse. But he curse mutates random dragon eggs into Spawn (3.5 monster manuals for reference).
Of the relatively few dragons who experience this terrible mutation most are distraught. As time goes by more and more dragons of either alignment flee to the old world to escape the doom of their young.

Storm Sorcerer Arcturus |

For my suggestion, I'd almost say borrow a page from the Dark Souls lore book; a kingdom built upon legendary dragon slayers. For whatever reason, the kingdom went silent for ages, and then suddenly, the dragon's fears are confirmed; the dragon slayers have returned, and their slaughtering advance is nigh unstoppable.

tsuruki |

tsuruki wrote:God's WHAT is threatening?God's.
God's are allways threatening.
Not a native speaker -.-
.On the note of scared Dragons, you could also make it the death of an especially prominent dragon, such as (this is custom so bear with me)
Vixaris the Heeded watcher.
This badazz caught the winds of change that brought about a cataclysm in the age of dragons, and facilitated their travel to safety. Once all the preparations had been made, he conducted a ritual with a dark secret, at the rituals ultimate moment of triumph, as every dragon in the world and just been moved between realms the great Vixaris closed the gate behind them, leaving himself stranded on the other side to take on the secret task he knew that had to be done for the good of all creatures remaining on the original world, stopping the cataclysm.
Apparently, his task succeeded, for indeed the player characters themselves tread upon the soil of the world he saved, but now, ages later, the dragon is dying. His children and allies on the new draconic home-world communicate with him, and plot to return to the material plane.
Of course, many secrets are not quite clear. Exactly what was the cataclysm and why did Vixaris send away his entire race before stopping it? Why is it that the dragons so fervently migrate to the material plane? And how can the PC's help solve any of these problems?