They discover a planar gate toward other world, and this is also being visited, explored, conquered or coloniced by people from Jackandor or the Mystaran hollow world.
Signs of the evil elemental eye cult have been discovered.
There is a secret war in the "land within the wind", the lord faes against the elemental titans.
A warlord is using totem shamans for an army of bug kaiju monsters.
The noble houses are secretly guided by shamans who can speak with the spirits of the ancestors.
A mad wizard is using spynewyrms to craft a new symbionts.
Waves of refugees from an unknown zone appear. Really they are petitioners, souls from the afterlife returned to the material plane.
A crashed alien ship is found in the dessert. The crew are shardmins who awakes. Their missions is to search and destroy the puppeters (mind-controlling parasites) and getting ready to be in the middle between a war between a rogue pirate gith faction and the cult of Thoon (Monster Manual V).
Shadow spiders are used elves to create a new race of slaves who worked in the underdark, but these can start a rebellion thanks a binder who uses vestige pact magic to speak with the Weaver Mother.
A meteorit crashed in the dessert and can infect living beings into mindless living-construct hordes, like the creatures from Metal Gear Survive.