Articuno Hatch a mystery egg in the upper left corner of the map (in the waterfall) (Articuno can hold or drop a frozen feather)
Zapdos Hatch a mystery egg in the lower left corner of the map (near the shop in the electric storm) ( Zapdos can hold or drop a power supply)
Moltress Hatch a mytery egg in the lower right corner of the map (where the fire is) (Moltress can hold or drop the flame of Moltress)
LUGIA Get a pokemon that has strength as ability (like Charizard). Make sure you get a frozen feather by killing Articuno (has 25% chance of dropping it). Use strength near the boulders in the water zone (close to a cave entrance). Enter the cave, and walk near the trees. The trees will disappear (so will your frozen feather) and walk further. You will see Lugia now. (Lugia can hold or drop a Lugia essence)
CELEBI Use the mysterious eggs in the lava or waterfall or powerplant to get legendary birds and kill two ancients to get celebi.
I think if you get a fossil? you take it to the fossil maniac and you get a omanyte or kabuto. <------ This is completely based off of what I think it is not proven. or Kill the 2 trees in the grass area (at the top right of the map). For that, you should use a good psychic pokemon. Then Celebi will come. (Celebi can hold or drop a strange egg)
GROUDON 1st destroy the boulders at the soutwest corner of the fire area, the cave will open. you need a lvl 10 moltress (or someone else with fire spin) and two other level 10 pokemon. use moltress's firespin to remove the barrels. then hatch an egg at the entrance of the gate that says mmm babies. then catch him!
Ho-Oh Make sure you kill all three legendary birds (Articuno, Zapdos and Moltress) and get the flame of Moltress from Moltress. Then go to the middle right of the map, where the burning house is. You will be able to go in. Walk towards the door, and kill the second door that blocks the way (that one is vulnerable). Walk further, DO NOT GO INTO THE PORTAL! Go right, and you will see Ho-Oh. (Ho-Oh can hold or drop a Ho-Oh essence)
Mew Get 3 mysterious eggs and 1 pokepouch (free capture is also handy). Go to the upper right of the map, where a cave entrance is with a door in front of it. Wait till it's night, then the door will disappear. Go as far into the cave entrance as you can, and use the 3 mysterious eggs. Then use the pokepouch. Mew will appear after a short while.
Mewtwo Make sure you get Mew, the Ho-oh essence and Lugia essence. Give Mew the 2 essences, and Mewtwo will appear. !WARNING! you will only be able to have 2 pokemon because Mew will disappear!!! MAKE SURE YOU HAVE 1 OPEN POKEMON SLOT!
Manaphy Make sure you get 2 frozen feathers from Articuno. Also make sure you get the strange egg from Celebi. Go to the psychic pokemon zone and go into the small puddle with those black things in it. The frozen feathers will disappear, and the egg will hatch into Manaphy. !WARNING! Manaphy will have a stats swap ability. It's very useful, but it will ruin the game for the people you swap stats with.
KYOGRE Catch Magikarp.
Use Magikarps splash attack to cool down fossil maniac who is digging fossils at the bottom of the map on normal pokemon area. Pick up the item.
Use the item near kyogres passage in order to swim across the water area. Then click the switch to teleport to kyogres gate.
Use pokepouch near kyogres gate where it says "hungry". You need enough kills in order to be "strong enough" to catch kyogre. Also having 3 ten level pokemons helps.
DEOXYS At the bottom of the map, look in the grass area shaped liked an arrow. Dig. You should find the glowing stone.
Bring the glowing stone on the top portion of the map. Approach the the group of rocks in the middle. A rock will fall on you converting the glowing stone to Meteor.
Store it in your Pokemon's inventory
Hatch a mysterious egg near the power plant. Kill Zapdos. There's a percentage that it will drop the power supply. Put it again in your Pokemon's inventory.
Direct your Pokemon to the Power Plant, the power supply and meteor with it. Use the Power Supply.
Laser Beam will attack your Pokemon but don't worry. Approach it and wait until Deoxys appear.
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