My campaign's current metaplot(s) is as such:
► The world is made of matter/energy that is created by the sun, known as Prime. Prime's fire creates this matter and disperses it around itself, allowing for the existence of the various planets in the cosmology, including the one the campaign takes place on.
► Matter and energy are one and the same, albeit in different aspect. The biggest part of the matter/energy created by Prime is known as leï, and it is what souls, life, death, magic, the planes, and the gods themselves are made of.
► But every fire needs a fuel. What Prime burns out to create existence is the utter nothingness of the Nihil (the Far Realm).
► The non-existing-yet-existing creatures from the Far Realm are not non-unhappy with the not-nonconsuming of their realm into dreadful existence. They wish to extinguish Prime so that the Nihil can reclaim all its non-matter that was twisted into being by Prime's fire.
► On the darkest world, Lerebre, the one the furthest away from Prime and thus the closest to the boundary of the reality pocket that makes up the setting's cosmology, an alien race of dreadful tyrants and savants (the Silians, aka cranial vampires or encephalon gorgers, from Tome of Horrors 2) explored the Nihil, and came back... Twisted (even more so). Those that came back where the foul pawns of Annihilation, and are intempt on extinguishing the Sun. They are known as Illithids. (Ceremorphosis on a Silian always result in an Ulitharid.)
► While Illithids may not succeed in extinguishing the sun any time soon, their mere existence is already a threat to the whole universe, as with every brain they devour, they "digest" the soul energy into a form more compatible with the Nihil. This process is further continued once the illithid joins the Elder Brain, which properly annihilate the contained "predigested" leï to return it to the Far Realm.
► Since then, the Silians and Illithids have waged war.
► But Illithids are not the only one who knows the connection between souls, leï, and the planes. The Fiends know of this, too, and each soul they corrupt is one more building brick in the creation of their home plane. In the center of the PC's homeworld, lies a hollow earth that's slowly crumbling, an inverted world inhabited by daemons, where everything hangs down from the ceiling and overlooks an unending pit bathed in sickening vapors. Every once in a short while, rocks and buildings detaches themselves and fall in the Cataract. These everfalling meteors are claimed be demons, who wages continual wars on them, "driving" them into colliding other blocks (cf. Acheron). Eventually, even eternity ends, and the meteors collide into the devils' eggworld, whose mass increases with each strike. The demons are always trying to damage Hellish structures, but in the end, it doesn't change anything.
So daemons are slowly corroding the world to destroy it because that's in their nature, demons just revel in the mindless chaos that results, and devils are building a Hell from the ruins. The physical aspect of the process is just the reflection of the metaphysical process. And in the end, the Fiends' new world will hatch from the hollowed husk of the old world, destroying everything on the surface in the process.
So there I have two similar metaplots. 1: Fiends trying to destroy the world to create their own, and 2: Far Realm pawns trying to destroy the whole universe because they see is as a pebble in their shoes. Both using murder, corruption, possession, sacrifice, and insane cults to further their own ends.
PCs are already discovering 1. Hopefully, this should let them recognize 2 later on.
Then you have submetaplots, or metasubplots, etc. that graft themselves on the main metaplots. For example, the kaorti invasion. The Kaorti's story is exactly the same as the Illithids, creatures who wanted to explore what's beyong the universe, and got turned into pawns of the Nihil, with the mission to reclaim all that matter for unbeing. The Ethergaunts have decided to protect the universe by slaughtering everyone and everything because they, alone, are immune to the Far Realm's corruption (or so they think), while the existence of any other creature is a threat to the cosmology. Feuds between the three category of fiends happen, as well as many other unrelated plots.