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Secrets brought to you by 
Battle Steven, the former champion.
After beating the Elite Four, a new part of Meteor Falls opens up. It is in the northwestern corner where you found Iron Tail. A new cave was made and you'll find Steven in it. His Pokemon are in the high 70's.
Compound Eyes Second effect
If you have a Pokemon with Compound eyes 1st in your Party it will drw Wild Pokemon that has held Items more often.
Cut's Out of Battle effect
Have a Pokemon use CUT to remove grass where wild Pokemon live. It will remove the chance of encountering wild Pokemon. The grass will regrow once you leave the area or enter a building.
Cute Charm's Second Effect
If you have a Pokemon with Cute Charm 1st in your Party it will more likely draw Wild Pokemon with the opposite gender of the Pokemon with Cute Charm.
Faster hatching eggs
Simply put a pokemon with the ability Flame Body or Magma Armor on your team to cut the amount of steps needed to hatch an egg in half.
Get the Mental Herb
In one of the treehouses in Fortree City is a man with a Wingull. Talk to the Wingull, and it will fly off out of the treehouse. When you get to Mossdeep City, you will see a person with a Wingull. Talk to it and it will fly off as well. Then go back to Fortree City and into the treehouse where you talked to the first Wingull. Talk to the man next to the Wingull, and he will give you the Mental Herb, and item which is a hold item that prevents attraction on the Pokemon that is holding it.
Hustle's Second Effect
If you have a Pokemon with Hustle 1st in your Party it will draw Wild Pokemon that has a Higher Level than the Pokemon that has Hustle.
Inherit Pokemon Natures through breeding.
To do this you need an Everstone. To get one, search in Granite Cave for a lone rock on top of a plateau. Once you get an Everstone, let the a Ditto or a female Pokemon that you are breeding hold on to it. Once you receive and hatch the eggs, the offspring will have a 50% chance of inheriting the Nature from the Pokemon holding the Everstone.
Intimadate and Keen Eye's second ability
If you put a Pokemon that has intimidate or Keen Eye 1st in your party the chances of wild Pokemon encounter is reduced by 10%.
Lightningrod's second ability
If you have a poke'mon with lightningrod as an ability, you will get calls from registered trainers more often.
Magnet Pull's secondary effect
If you have a pokemon with the Magnet Pull ability in front of your party, it increases the chances of finding wild steel-type Pokemon. This is very useful for finding rare steel types, such as Mawile.
Mirage Island
Mirage Island is an invisble Island located on Route 130. Most of the time it will be invisible but on rare cases, the island will be visible. To find out if the island is there or not, go to Pacifidlog Town and talk to the old man in the bottom right house looking out the window. He will tell you wheter the island is there or not. The cause is unknown so a bit of luck is needed to find it. On the island you will find the rare Leichi Berry that powers up your Pokemon's attack in battle when it gets weak. In the grass, you will only find Wild Wynauts.
Mystery Gift
To unlock mystery gift, go to a pokemon mart and press A on the piece of paper on the counter. Then insert the words LINK TOGETHER WITH ALL. Press select to easily find the words. After this the store lady will talk to you and tell you that mystery gift is now unlocked.
Static's secondary effect
If you have a pokemon with the Static ability in the front of your party, it increases the chance of finding a wild electric type pokemon. This is EXTREMELY useful for finding rare electric types, like Pikachu in the Safari Zone.
Suction cups/Sticky hold's second ability
If a poke'mon in your party has suction cups/sticky hold as an ability, then you will have an easier time fishing for wild poke'mon.
Swarm's second ability
The Pokemon ability Swarm has 2 effects. It raises Bug-type attacks by 150% when the user is weak, and, new to Emerald, it makes pokemon cry in the background more often. For example, in caves outside of battle, you will hear a Pokemon screech more often.
Synchronize's second ability
If you have a poke'mon with synchronize as an ability, you will encounter more poke'mon with the same nature as the poke'mon with sychronize. Note that the poke'mon with this ability must be in the front of your party.