The Seafloor Cavern (Japanese: 海底洞窟Seabed Cavern) is a location in Hoenn, deep beneath the water of Route 128. After surfacing inside the cave, there is a maze of tunnels to the deepest part, where the super-ancient Pokémon resides.
In Pokémon Ruby, Sapphire, and Emerald, the stolen Submarine Explorer 1 is parked at the bottom of the underwater area underneath the Seafloor Cavern. In Pokémon Omega Ruby and Alpha Sapphire, the stolen Submarine Explorer 1 is parked at the shore in the entrance chamber of the Seafloor Cavern.
In the deepest part, MaxieROR or ArchieSEAS will attempt to control the super-ancient Pokémon using the orb he stole from Mt. Pyre. However, the Pokémon does not respond well, and instead will escape, causing harsh sunlightR/extremely harsh sunlightOR or rainS/heavy rainAS throughout eastern Hoenn; in Emerald, both rain and harsh sunlight appear, alternating back and forth at regular intervals.
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, PrimalGroudon 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 Team Aqua Grunts went deep inside the cave and found a room where Kyogre 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.
In The Beginning of the End with Kyogre & Groudon II, Maxie awakened Kyogre and Groudon by using the Red and Blue Orbs, intending to give Groudon the advantage. However, in Very Vexing Volbeat, Maxie started to struggle, as controlling two Legendary Pokémon at the same time started to take too much of his mental capacity. As such, he had the Blue Orb be taken away by Tabitha so that he could focus on controlling Groudon. While doing what he had been ordered to do, Tabitha was ambushed by Amber, who used his Volbeat's Trick to steal the Blue Orb and deliver it to Archie. Archie then locked both Amber and Tabitha inside the Submarine Explorer 1 and sent it to dive on autopilot without its heart component in order to do away with the men inside.
In No Armaldo Is an Island, Ruby and Sapphire reached the Seafloor Cavern thanks to Sapphire's Relicanth, Relly. They started battling against Archie and Maxie, but were unable to retrieve the Orbs before the two villainous team leaders were overcome by their power and ended up fusing with them. Maxie and Archie then grabbed Ruby and Sapphire, and started to fly away, the Orbs' powers being called by Groudon and Kyogre.
In It All Ends Now V, Kyogre was revealed to have returned to slumber in the Seafloor Cavern, while Groudon had chosen to sleep inside Mt. Chimney instead.