Labyrinth

Labirynth is the most insane feat of engineering ever attempted by any mortal species inhabiting the Prime Material World. It is an effect of several thousands of years of hard works of the inhabitants of the ancient Sekarkan Empire, on that eventually became the safe haven for the Empire's inhabitants when the Dominance Wars ended with the victory of the ancient dragons.
With Sekarkans no longer able to challenge the First Empire's dominance over the skies and the surface, there was only one place for them to retreat to, the only place where the dragons couldn't follow them - the darkness beneath the surface.
As a result, the Sekarkans used their great magical might, massive manpower and architectural knowledge to carve out a maze of tunnels beneath the surface of Karadia, at this point the only part of the surface still held by the ailing Serkarkan Empire. As the forces of the dragons continued pushing, the maze kept growing deeper and deeper, with more and more of Serkarkan population moved underground.
Eventually, all of Sekarkans have moved underground, abandoning the surface forever. This forced the Labyrinth to expand, and with the magic of the Empire reaching its limits, it could no longer expand the habitable zone any deeper. As a result, the expansion was horizontal more than it was vertical, with Sekarkans creating smaller, satellite-Labyrinths connected to the main one, their population spreading from Karadia to Telya, Arrica and some fragments of Arzia.
Some scholars suspect that their goal was to grow their numbers and eventually take the surface back from the First Empire. If that was the goal of the descendants of Sekarka, they failed, their entire empire being devoured by an unknown magical disaster that was caused by a failed project for mass ascension into a higher state of existence (or perhaps an attempt to improve themselves as a species.
Labyrinth, their greatest creation, however survived that and exists to this day as the monument to the greatness of the ancient Sekarkans.

Geography

To call the Labyrinth a 'cave system' is a massive, almost comical understatement. It is a second world underneath the one known to the inhabitants of the surface, one as alien and terrifying as it's aweinspiring and sometimes surprisingly mundane.
It starts at the depth of about 150 meters beneath the sea level, and goes deep. Very, very deep. No one is certain just how deep it actually goes, with the deepest recorded location [ancient Sekarkan fortress known today as Belzar's Fall] is located approximately thirty-two kilometers underground. The Labyrinth is believed to go much deeper than that, with central square of Belzar's Fall involving a giant and long-defunct elevator leading downward.
Those thirty-two kilometres are divided into thirteen layers, each covering approximately 2,5km of depth. This is only the case for the main Labyrinth under Karadia. Telyan one has only seven layers (with the deepest known point being at around 17km). The sub-Labyrinths under Arrica and Arzia were never appropriately investigated, but it is believed that they're even less deep than the one under Telya.
Those layers have more meaning than just the measurement of depth. Maintaining a livable conditions thirty-two kilometers underground requires immense amounts of magic. As all mages can tell if asked, it's not carving out the Labyrinth that's truly the most mindboggling feat of the creators of Labyrinth - it's the magical side of it, one that managed to largely remain functional to this day.
Sekarkans imbued nearly incomprehensible amount of pure magic into the very space of the Labyrinth, in order to keep the temperature, air composition and lighting on what could be considered livable conditions for former inhabitants of the surface. To this day, overwhelming majority of those spells is still holding, keeping the temperature of the Labyrinth at anywhere between 20 to 30C, its air to be breathable and filling the corridors and halls of it with ambient lighting that keeps the place reasonably lit with artificial sunlight that lets plants grow. The same magic also suppresses the effects of earthquakes, rendering them largely muted when compared to other places and preventing the Labyrinth from collapsing.
What's the problem with that and how does this make the layers into a very important thing? The deeper you go, the more the ancient magic has to alter reality in order to make the Labyrinth livable. This translates into a steadily raising density of ambient mana, that results in more and more dangerous and powerful things stalking the tunnels and being able to exist there permanently. This culminates in the Hollow, a parasitic growth on the Reality in the shape of a warped, malformed Spiritual World, controlled entirely by the forces of Pentagram.
What's more, every layer in the Karadian Labyrinth was established by a subsequent wave of refugees from the surface, usually from a different part of the surface dominion of Sekarka that was seized by the First Empire. They were separate provinces of the underground Sekarkan Empire that just happened to coexist vertically instead of horizontally. As a result, layer transitions are relatively rare and spread wide, most of them being heavily fortified even back in the times of the Sekarkan Empire, resulting in every layer being a separate world.
What also has to be mentioned is that there are whole segments of the Labyrinth where the magic keeping them habitable has to certain degree failed. There are hundreds of square mile of the Labyrinth that are completely pitch black, that have temperature either pushed above or beneath the designated norm, where earthquakes caused entire sections of it to cave in or where the air is unbreathable or downright toxic. High ambient mana quotient often stopped from becomingcompletely uninhabitable and instead had them warp into various alien environments.

Layers

The Shallows is where the Labyrinth starts. It's a section composed of layers one to four that are also known, at least in Karadia, as the Nearsurface, the Oversee or Highlight. It is also often expanded to involve the unofficial layer zero, later additions to the Labyrinth created by underground civilizations digging upward in order to establish contact with the surface.
As one can expect, the Shallows are inhabited by civilizations that are usually heavily connected to the surface, most if not all of them being client states of the Grand Empire of Karadia and heavily penetrated by the imperial culture and religion, not to mention being economically tied to the surface The environment is also usually rather tame, even if it still involves many elements that might appear completely alien to the surfacers visiting the Labyrinth.
With the pressure applied on the sekarkan magic keeping this place habitable being very small, the damaged segments are almost unheard of.
The Lower Sea comes next, also known as the Sekarkan Sea, the Sea Beneath or the Dark Sea. It is a part of the Labyrinth composed only of the fifth layer, and only exists in Karadian labyrinth. It's also considered by many to be the most shocking and insane parts of the Labyrinth, which is already considered shocking and insane by many to begin with. Why?
Because it's a massive hollow filled with water. A lot of water. The Sekarkan Sea is quite literally a sea hidden entirely deep under Karadia, almost as large as the continent above it. The only pieces of solid ground here surround the rock pillars (some of them many kilometres wide) supporting the ceiling and usually holding passages and elevator shafts connected the fifth layer with both fourth and sixth one. With the Dark Sea being extremely calm due to lack of winds and generous application of magic, the sea is generally considered to be one of the fastest way of traveling form one edge of the Labyrinth to another, with many ships prowling its waters.
It has its own vibrant fauna and flora, most of it aquatic. There are also pillars that no one likes to come too close to, for a variety of reasons. What's more, there are also islands here - some of them inhabited, but many aren't, especially those located far away from established trade routes. Some are still waiting to be found by explorers, some however belong to the category of places unknown to the mortals because those that find them never come back to tell the tale.
By all calculations of the Imperial Magic Guild, this place shouldn't exist, Sekarkans removing so much rock that the entire continent above (or at least large parts of it) should collapse underground. Whether it didn't because Sekarkan magic keeps it up or whether the entire place is a separate plane of existence woven so masterfully into the Prime Material World that no one can find the seams remains a mystery.
The Warrens also known as the Undersee or Lowlight, start when the Lower Sea ends and covering the area between the sixth and tenth layer. This is where things become really interesting, and rarely in a good way. The mortal control over this zone is tenuous at best, with the civilizations scattered throughout the Warrens usually having little interest in the surface that to most of them remains little more than a fable, a tale of an alien land on the other side of the world that will never truly become important to them.
The result of that is many scattered city-states, tribal territories or semi-civilized countries, existing in the gray area between the Shallows (that are heavily influenced if not downright control by the High Gods) and the Depths that are effectively controlled by the forces of the Pentagram. Entire regions here are on the verge of collapsing into the Lost Lands, or remain nearly unexplored, hiding treasures beyond mortal comprehension and unescapable doom in equal proportions.
Often it's the local fauna and flora - and the wide-scale malfunctions of life support magic - that's the biggest obstacle that the Pentagram armies emerging from the Depths encounter on this level, which is perhaps the best image of just how incredibly dangerous this place is.
The Depths is the deepest part of the Labyrinth, composed of layers eleven to thirteen. It has nearly entirely fell under the control of the forces of the Pentagram, although it's yet to be fully incorporated by the Hollow. As a result, the Depths are still a part of the Prime Material World, making them at least theoretically follow the rules and laws of it.
As a result, it's still inhabited by mortals, most of which are doing their own human things. However, their civilizations has been fundamentally corrupted by the Pentagram, making their inhabitants lost in body, mind and soul. It's often best to imagine them as daemons of the Pentagram that are unaware of their status, pretending to be mortals yet not even knowing that they're pretending.
There is no saving them. There is also no civilization of the Depths that isn't incredibly evil, warped, horrid and downright eldritch by the standards of not only the surface but even the inhabitants of the Warrens.
The Hollow lies beyond the Depths. Where exactly can one enter it? How exactly is it connected with it? Is it truly beneath it in the geographic sense of the word? Is the unknown, unexplored abyss beneath the Belzar's Fall a part of it or something completely different? No one knows, for no one has ever reached the Hollow and returned from it while being able to describe what the've seen there.

Ecosystem

The ecosystems of the Labyrinth are too diverse to describe. There are hundreds of different ecosystems there, living in mana-rich environment that changes most of local liveforms into beasts. Some of these ecosystems grew in environment absolutely alien to what lives beneath the sun. Spelunkers tell tales of mushroom forests, caves filled with acidic lakes, places that seem to exist in additional dimensions...
There are also entire places that no one knows how to classify, but some suspect them to be evidence for the theory that the Labyrinth is changing into Lost Lands. Breaches into alternate realities and another worlds. Caves that are alive. Places that bleed. Areas where crystals breathe. Things that deny description. The deeper one descents, the more insane his surroundings become, but only at the deepest level of the Warrens the reason for that is actually the Pentagram.
There are also the deep gods, a variety of powerful and apparently religiously unaligned supernatural entities classified as either widely divergent fae, extremely powerful beasts or archdaemons (but most appear too strong for the last category, and are more of a demigod-level threats). Some speculate that they are the ancient deities of the Sekarkan Empire, or perhaps their equivalent of magisters that has transcended mortality so long ago that they themselves forgot their mortal past. They are often worshipped by the civilizations of the Labyrinth, but those living in the deepest levels are increasingly corrupted by the influence of the Pentagram.