From Bulbapedia, the community-driven Pokémon encyclopedia.
Now that the Elite Four has been defeated it is time for you to see all the remaining things that can be done at this point.
Eon Pokémon
Once you start your save file again you should be in your room at your house in Littleroot Town. Go downstairs and your father should be there. He gives you a present from your old friend Mr. Briney, the S.S. Ticket for the S.S. Tidal and suggests you go to the Battle Tower, before leaving for the Petalburg Gym. Also look at the TV and it states their is a flying Pokémon traveling around Hoenn which is LatiosWrong template. See Template:Sup/doc. or LatiasWrong template. See Template:Sup/doc.. From this point on you have a chance of finding one of these Roaming Pokémon, whose primary color is the opposite of the game color of the version you are using (Blue for Ruby and Red for Sapphire). To get the other one you must use either the other version or get the event-exclusive Eon Ticket to Southern Island, a special Nintendo event-only island.
It is recommended to use Fly around a city that doesn't have too many exits and use it as often as necessary and bring plenty of Max Repels with a Pokemon that is slightly under level forty to be able to encounter it so your Pokédex is capable of tracking it afterwards if you do not wish to use the Master Ball.
S.S Tidal
With the S.S. Ticket in your hand you can board the S.S. Tidal in Slateport City or Lilycove City. This ship can transport between both cities or to the Battle Tower. If you choose the Battle Tower there it quickly takes you there, but if you choose either of the two cities you can actually go inside of it.
The S.S. Tidal is in command of old friend Mr. Briney who previously helped you got across the ocean between Slateport, Dewford City and Petalburg City. Mr. Briney was made the honorary captain by Captain Stern (though it was first referenced if you head to Stern's Shipyard in Slateport after the Team MagmaWrong template. See Template:Sup/doc./AquaWrong template. See Template:Sup/doc. encounter).
Trainers (Cabins)
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Trainer
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Pokémon
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Trainers with a Vs. Seeker by their names, when alerted for a rematch using the item, may use higher-level Pokémon.
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Trainers (Basement)
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Trainer
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Pokémon
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Trainers with a Vs. Seeker by their names, when alerted for a rematch using the item, may use higher-level Pokémon.
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All you need to do on this ship is sleep in your cabin, to be allowed to leave the ship, though you do have the option of challenging trainers.
You can also go collect a few items namely TM49 (Snatch) from the cabin directly above Cabin 4 or the Leftovers hidden in the trash in the upper left corner of the basement. Other than that there is nothing else to do inside of the S.S. Tidal. After resting in your room a few times, the announcement will be made that the ship has arrived in whichever city you are headed to.
Battle Tower
Once you make the request to head to the Battle Tower in Slateport or Lilycove Harbor you will automatically arrive. This area is the only closed off area of Hoenn that is accessible by ship and once you are here only the ship or Fly can take you back to the main areas of Hoenn.
The battle tower is designed to test your skills as a player and can give you a trainer star if you win 50 in a row. The battles involve single, double, or linked up battles. Other than that there is no other function that the player tower has. Here is the list of those banned from use.
Sky Pillar
When ready head to Route 131 (Look here for any details on this Route or those around it) and head north into the Sky Pillar.
Available Pokémon
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R
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S
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E
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1F, 3F, 5F
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48-56
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30%
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R
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S
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E
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1F, 3F, 5F
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34-35
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30%
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R
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S
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E
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1F, 3F, 5F
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48-56
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30%
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R
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S
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E
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1F, 3F, 5F
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33-34
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30%
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R
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S
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E
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1F, 3F, 5F
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48-56
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30%
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R
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S
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E
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5F
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54-60
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6%
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R
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S
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E
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5F
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38-39
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6%
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R
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S
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E
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1F, 3F
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47-56
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25%
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R
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S
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E
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5F
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48-56
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19%
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R
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S
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E
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1F, 3F
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36-38
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25%
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R
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S
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E
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5F
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36-38
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19%
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R
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S
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E
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1F, 3F, 5F
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48-56
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15%
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R
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S
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E
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1F, 3F, 5F
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37-38
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15%
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R
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S
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E
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1F, 3F, 5F
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48-56
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15%
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Special Pokémon
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R
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S
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E
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6F
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70
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Only one
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A colored background means that the Pokémon can be found in this location in the specified game. A white background with a colored letter means that the Pokémon cannot be found here.
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Once you get past the entrance you should reach the building. You will need to use the Mach Bike to get to the top along with skilled timing to get past the cracked floor. It would be smart to bring some Max Repel to avoid unnecessary battles while concentrating on using the bike.
On the 2F there should be some difficulty but all you have to do is head for the other door, and only worry about making a few well timed sharp turns. The 4F is more difficult however, you must move south, then quickly move west, at the last part of the south area of the room you have to quickly move north without stopping at the rock. Lastly without moving too slow or too fast to overshoot it, move to the cracked area in the middle and fall down to return to the 3F and use the stairs there to get back up, then you can travel to the 5F. Just be patient on both these floors since it will take some time before you can pull it off successfully.
Once you reach the 6F you will find the legendary Pokémon Rayquaza. Rayquaza is the highest level Pokémon you will find in the game, and unless you have a Pokémon that is around that level then a Master Ball is necessary.
Pretty much this is all that the game has to cover so this all there is to this quest in Ruby and Sapphire and only the Battle Tower can offer a challenge at this point.