Seafloor Cavern/Anime

Pokémon Generations
The Seafloor Cavern briefly appeared in a vision by Courtney in The Vision. Although the interior of the cavern wasn't shown, the top was depicted as a rocky island protruding from the water. At this rocky island, Primal appeared and attacked Team Magma.

It properly appeared in The Cavern, where it was shown that Team Aqua also visited it. Archie, Shelly, and three s went deep inside the cave and found a room where was resting. Archie woke it up with the Blue Orb, after which Kyogre transformed into Primal Kyogre and started to go on a rampage throughout the Hoenn region.