Connected to the ocean, the appearance of Shoal Cave changes with the tides. Seawater floods the cave during high tide, closing off some areas and opening others. It then drains away during low tide, revealing new areas for exploration. The tides change every six hours, at 3:00 and 9:00.
An old man in the entry chamber offers to make a Shell Bell for your Pokémon. But first, he needs you to collect some of the cave's natural resources: Shoal Shells and Shoal Salts. These items are replenished each day, so there's no limit to the number you can collect. Once you hand over four of each item, he crafts the health-restoring item for you. Surf northwest and take the doorway there to reach the next chamber.
Surf along the water in a clockwise direction, collecting the four Shoal Shells and a Rare Candy on the way. Take the southeast doorway back to the entrance, where you can collect a Big Pearl on the nearby ledge.
An old man in the entry chamber offers to make a Shell Bell for your Pokémon. But first, he needs you to collect some of the cave's natural resources: Shoal Shells and Shoal Salts. These items are replenished each day, so there's no limit to the number you can collect. Once you hand over four of each item, he crafts the health-restoring item for you. Head through the north doorway to reach the next chamber.
Head up the stairway, go north and climb down the east-central ladder.
Grab the Shoal Salt and Ice Heal, then climb the hill to the ladder in the northwest.
Go west then south along the two bridges, then climb down the ladder in the center.
Head east to meet a Black Belt and receive a Focus Band from him. Continue east to find another Shoal Salt, then use Strength to move the boulder eastward and descend the ladder to the south.
The final cavern is permanently encased in ice, and the slick floors hinder travel. Go south from the ladder, across two ice patches. At the third ice patch, slide west to the second snow patch within it. Slide north, then west and south to the third small snow patch. Slide south, east, then north to continue on. Slide north to the snow patch near the narrow stairway. Move west then south to a rock, then east and north to the central plateau and the NeverMeltIce on its south end. Slide south from the narrow stairway, then west and north to reach the northwest corner. Go east then south to a snow patch, then north to a rock near the room's northwest corner. Head east, south, and west, then move north, west, south, and west to the small snow patch. Slide north, east, then south to reach TM07 (Hail) and jump the ledge to return to the ladder.
Head for the south-central cabin. Seawater has flooded into the room, so use Dive to traverse an underwater hallway that leads to an isolated part of the ship.
This part of the ship has six cabins. Rooms 1-3 are located on the south side, and Rooms 4-6 are found to the north. Four of these rooms are locked, and although Room 5 is unlocked, there is debris blocking the door.
Enter Room 3 to see a sparkle on the floor; this signifies a hidden item. Pick up the Rm. 1 Key from the northeast corner, and the Water Stone to the left before leaving.
There are two hidden items in Room 1. The Rm. 4 Key is located near the west wall, while the other item is just trash. The visible item is TM18 (Rain Dance).
In Room 4, inspect the trash can in the northeast corner to find the Rm. 6 Key.
Enter Room 6 and collect the Luxury Ball, then use the narrow hallway to reach the adjoining room. Room 5 has three pieces of trash and one item; the Rm. 2 Key is located three steps south of the left-hand trash can.
The long-forgotten Seafloor Cavern can only be reached from an underwater cave in the depths of Route 128. Archie has gone to great lengths to breach the seal that has protected this place for ages, in the hope of awakening the super-ancient Pokémon rumored to dwell here. He believes this Pokémon has the power to bring about the great future he desires, but the risks seem far too great.
When you first enter the cavern, you find Captain Stern's sub moored beneath the waves. Rise to the surface and take the north doorway to the next room.
This room features two boulders that hinder travel. Go northwest and clear the way with Rock Smash, then use Strength to move the first boulder southward. Head east and move the second boulder eastward. At this point, there are two paths forward. The northwest doorway leads directly to the southeast part of Room 4. The southeast doorway leads through Rooms 2 and 3 to the southwest part of Room 4.
Head south to a fork in the road. Both tunnels lead into the next room, but the western tunnel serves as a shortcut.
The doorway to the south merely leads back to the entrance. Instead, go through the northeast doorway.
Use Strength or Rock Smash to clear a path, then move the west-central boulder to the northwest corner. The northwest doorway leads to Room 5, while the northeast doorway leads to Room 6.
This room has many strong water currents. Surf out into the water and ride the currents to a calm spot a short distance to the northeast. Sail east to ride the current to a patch of calm water to the northeast. Go east again to follow the current around the rock outcropping to the west side of the room. Surf westward and take the current to the northwest doorway.
This room has many strong water currents. Surf eastward along the south wall to the second current, which leads a short distance northward. Go north from here to reach the west side of the room. Sail north once more to follow the current back and forth on the room's north side. Climb onto shore and go through the northwest doorway.
The room splits into two tunnels before converging near the next doorway. The room's east side is littered with boulders, while the west side is clear, aside from Shelly and an Aqua Grunt. She's looking for payback for what happened in the Weather Institute, and draws you into battle!
There are a dozen boulders here to block progress. Start off by moving the south-central boulder one step northward and the other two southern-most boulders farther apart. Push the first boulder one step westward, then shove the middle boulder one step northward. Move the boulders on the left and right farther apart, then push both the north-northwest and north-northeast boulders to the north wall. Finally, push the middle boulder to either side to reach the doorway.
Go east to find TM26 (Earthquake) on the room's highest level before continuing along the downward-sloping corridor. Team Aqua's driven leader, Archie suddenly runs up to you. Like Maxie did with Groudon, Archie has discovered the super-ancient Pokémon, Kyogre, and stands ready to restore the creature with his stolen Red Orb. With his plan so close to fruition, he's not about to let anything stop him, and drags you into battle.
Even defeated, Archie reaffirms his intent to revive the super-ancient Pokémon. While talking, the Red Orb suddenly shines brightly, awakening Kyogre. Like Groudon before it, the Pokémon flees. Just then, Archie receives an urgent call from his subordinates outside. The great energy generated by the legendary creature has altered and intensified Hoenn's weather as expected, but to dangerous, unforeseen levels. The weather's dramatic shift to a strange mix of heavy rain and harsh sunlight influences any battles on the region's east side. Maxie and a pair of his Grunts enter a moment later. He condemns Team Aqua's actions and tries to reason with Archie, who counters by criticizing Team Magma for disturbing Groudon.
The group returns to the surface, where they witness the extreme weather firsthand. Kyogre's power has surpassed expectations, forcing Archie to grudgingly agree to work with Maxie to set things right. Once the others leave, Steven swoops down to assess the situation. He informs you that the oppressive weather seems to originate in Sootopolis City to the northwest. He's headed there to investigate, and suggests you do the same.