R'lyeh is built as a complex maze of islands and canals linked by bridges and towers. It is unclear whether the city was always this way, or if it is a product of the cataclysm that sank it beneath the sea. While in Apocrypha, the city sits in an endless sea of poisonous ink, like the rest of Apocrypha. The city looks to also be completely submerged, although creatures can move about freely as if it was open air. The Hunter and Arsenath Moslin both conjecture that the city actually lies deep underwater on the sea floor, but that Yog-Sothoth uses his power to keep it partially within Apocrypha to protect the denizens within. When the city rises again it is mostly the same, but is damaged and collapsing from the geographical shift that pushed it from the seafloor. The island sits on a jagged mound of muck and stone that has been thrust from below, destroying parts of the city in the process.
R'lyeh is built in the same manner as other buildings associated with Apocrypha, implying a heavy correlation between the Cult of Cthulhu and the Cult of Miraak as offshoots of the same group, both heavily influenced by Hermaeus Mora. When the city rises again and the Cult begins to inhabit the city, they begin to build new infrastructure in more primitive wood construction built over the ancient stonework.
The city is built as a network of round islands build on heavy stone pedestals that stick up from the seafloor. Each island serves a different purpose, depending on the structure built upon the pedestal. Stone latticework bridges and stairs connect the pedestals. The denizens of the city live in tall, obelisk-like towers with a single, dome-like room at the bottom. The upper floors of the towers are likewise connected with a network of bridges, allowing circulation at multiple levels. Many of these islands and structures are ruined beyond recognition.
At the heart of the city sits the Vault of Cthulhu. It is in this massive enclosure that the dreaded Cthulhu is imprisoned within. It is here that sacrifices are given to Cthulhu, chained to the upper rim of the enclosure for Him to feed upon. Before the vault sits a broad plaza where the Cult prays and sacrifices to their Lord.
It is said that the Star-Spawn spread from Red Mountain and moved north to Solstheim, where they corrupted the Dwemer there. It is not known why or when they built R'lyeh further to the north, but it is there that Cthulhu made his home and ruled over his kin. When the Dwemer rebelled and pushed the Star-Spawn from Solstheim, Cthulhu came forth from R'lyeh and tore a path of destruction across Solstheim. The sea gods Tiamat and Phorcys , together with the Praenumidium, fought Cthulhu back to R'lyeh and locked him in his vault. Then Tiamat swallowed the whole city and plunged it beneath the sea, trapping the city and its hordes beneath the crushing depths. Even Hermaeus Mora could not free the city from Tiamat's clutches; he could only protect those within by partially shifting the city into Apocrypha. It was not until the death of Tiamat at the hands of the Dragonborn that the power that held the city trapped began to weaken.
- The decision to place R'lyeh in Apocrypha, instead of just physically underwater, was done deliberately, as Skyrim does not allow much freedom for exploring underwater. It was for this reason that the quest leads you to a small Deep One city that IS underwater, letting the player experience a bit of underwater exploration first, which then sends you to R'lyeh via the Necronomicon .
- The architecture of Apocrypha is very complex, and the city uses a LOT of static objects. This can be quite taxing on lower-end machines.
- Because of the complex meshes, the navmesh is complex (and badly constructed) which can also cause slowdowns. The mod author is working on fixing the problem.