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 will 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. Take a look at the TV— it states that there is a flying Pokémon traveling around Hoenn, which is LatiosR or LatiasS. From this point on you have a chance of finding one of these Roaming Pokémon. To get the other Eon Pokémon, you must use either the other version or get the event-exclusive Eon Ticket to Southern Island, a special Nintendo event-only location.
Since the Pokémon change locations, when a boundary is crossed (such as entering or exiting a building), one viable strategy for increasing encounters with the Eon Pokémon is to find a grass patch near a building, such as Route 117 near the Pokémon Day Care or the southern end of Route 110 near the entrance to Seaside Cycling Road. Use a Repel (of any strength) and bunny hop on the Acro Bike in the grass. If the Eon Pokémon doesn't appear within a minute or so, enter and exit the nearby building to change the area the Eon Pokémon is currently visiting, and repeat the process. Once you've encountered the Pokémon the first time, its current location will be visible in your Pokédex.
The Eon duo are frustrating to catch since they have the ability to run away from battle. This Pokémon is probably the best one to use your Master Ball on but if you already used yours or you don't want to, there are some strategies you can utilize. One strategy is to use Mean Look so the Pokémon can't escape. However, the Eon duo are fast and your Pokémon needs to be faster in order to use the move before it escapes so speedy Pokémon like Gengar and Crobat are recommended.
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 MagmaR/AquaS encounter).
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Pokémon
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Lady Anette
Reward: $9000
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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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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.
| Items
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Location
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Games
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TM49 (Snatch)
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Gift from a man in the cabin above cabin 4
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R S
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Leftovers
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Hidden in trash can in the upper left corner of the basement
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R S
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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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Games
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Location
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Levels
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Rate
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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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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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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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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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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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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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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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E
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1F, 3F, 5F
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48-56
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15%
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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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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 Repels to avoid your concentration on using the bike being interrupted by wild Pokémon.
On 2F you may have some difficulties, but all you have to do is head for the other door and only worry about making a few well-timed sharp turns. The fourth floor is more difficult, however— you must move south, then quickly move west, and at the last part of the south area of the room, quickly move north without stopping at the rock. Lastly, without moving too slow or too fast, move to the cracked area in the middle and fall down to return to the third floor. Use the stairs there to get back up, and then you can travel to the fifth floor. Just be patient on both these floors, since it will probably take some time before you can pull it off successfully.
Sky Pillar 6F, Rayquaza's chamber
Once you reach the roof (6F), you will find the legendary Pokémon Rayquaza waiting for you. Rayquaza is the highest-leveled Pokémon you will find in the game, and unless you have a Pokémon that is around level 70 with excellent Defense, a Master Ball will probably be necessary in order to catch it. You might want to come back to catch Rayquaza later, since you only have one chance to battle it!
You have now completed pretty much all that the game has to offer. The only real challenge left is the Battle Tower. If you win 50 times in a row, you can get a star on your Trainer Card. Additionally, if you trade with Pokémon FireRed and LeafGreen or Pokémon Emerald, you will receive National Pokédex upgrade. Game Freak employee at Lilycove's hotel will give you diploma for completing Hoenn Pokédex and another for National Pokédex (minus event-only Pokémon for both).
