Team Magma/Aqua have broken into the sealed Seafloor Cavern, where the super-ancient legendary pokémon of Hoenn was sealed.
In the Seafloor Cavern, you will need to use Strength and Rock Smash, as well as Surf and Dive, to go all the way through the cavern. Make sure to bring pokémon who know those moves.
Explore the Cavern
Once you enter the cavern, go into the light that is shining down, and press A to go to the surface.
In the entrance of the cavern, you will see the submarine that Team Magma/Aqua modified in order to enter the cavern. In this room, use your Dowsing Machine in the southeast corner of the cave to find a hidden Heart Scale.
Go north to the next room. Go north, then east, and use Rock Smash on the rock that is blocking your path. Then go east and use Strength on the boulder to push it east into the hole.
To the northwest, you can battle a Grunt. Go up the northeast stairs and then go southeast. There is another Grunt you can battle. Go south from that Grunt and go through the exit there.
There is a Grunt running around to the right of the entrance to this room. After you go past that Grunt, go south and use Strength to push the boulder south into the hole. From there, go southeast and through the exit.
Go south and jump down the ledge. There is a Grunt to the south that you can battle. Go east and jump down one of the ledges, and use the Dowsing Machine in the southeast area to find a hidden Escape Rope.
Go through the door in the middle of this room.
Use Strength to push the boulder north. Then go to the northwest corner of this room and use the exit there.
You will be back in the first room. Go north and down the stairs, and go past the Grunt. Then use Strength to push the boulder down, giving yourself a shortcut. After that, go north and through the door.
Go west and use Strength to push the boulder to the left until it falls into the hole.
If you want to open up all areas of this room, go northeast from the boulder that you just pushed and go up through the passageway in the middle of the room. Go to the left and push the boulder to the left until it is up against the small rock.
After that, go north through the narrow passage and push the boulder up. Then go east, then south, and use Rock Smash on the small rock to the right of the boulder.
Go around to the left side of this boulder and push it to the right until it falls into the hole. After that, push the boulder below it into the hole.
Then use the northwest exit of the room where you pushed the boulders around.
Use Surf and go northeast, into the currents that are going northward. When you stop, go west into the next set of currents. You will end up near the northeast corner of the room. Go through the northeast exit.
Go up the stairs and push the boulder to the east. Then use the southeast exit of this room.
Use Surf and go to the right side of the water. Enter the currents that are pushing downward. From there, go to the right or down. You will end up in front of a small island where you can get TM55 Scald. Go to the north side of the island and Surf north into the currents that are pushing northward. You should end up near the northwest part of the room. Go through the northwest exit.
Go north through this room. You have to battle the Grunt. After that, push the boulder south into the hole to give yourself a shortcut. Then go north through the exit.
In this room, push the two southern boulders into the holes that are next to them. Then push the southeastern boulder to the east, and push the southwestern boulder east twice. Go north through the middle of the room and go to the left, then push the boulder down. From there, you can push the northwest boulder north into the hole. Go north from there to reach the exit of this room.
Follow the path through the next room and TM26 Earthquake before you go down to the next room.
Battle the Team Magma/Aqua Leader
In the next room, go north. After a cut scene, you will have to battle the leader of Team Magma/Aqua.
In Omega Ruby, you will have to battle Maxie. He has a level 41 Weezing, a level 41 Crobat, a level 41 Mightyena, and a level 43 Camerupt that he will Mega Evolve into Mega Camerupt.
In Alpha Sapphire, you will battle Archie. He has a level 41 Muk, a level 41 Crobat, a level 41 Mightyena, and a level 43 Sharpedo that he will Mega Evolve into Mega Sharpedo.
After the Battle
After you beat the leader, watch the cut scene. When you go outside, you will find (in Omega Ruby) that the sunlight has turned extremely harsh, or (in Alpha Sapphire) that there is a constant downpour of rain. The leader of the opposing team will tell you to go to the Cave of Origin in Sootopolis City, and Steven will arrive and tell you to go there as well.
To go to Sootopolis City, go north to Route 127, then go northwest to Route 126.