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General Tips for Catching All Legendary Pokemon
All legendary Pokemon require a fairly similar capture strategy. Your team should always have two Pokemon with a high speed rating and specific move sets. Consider Gengar and Scizor. Equip Gengar with Hypnosis and Disable, while Scizor should have False Swipe. You could also have an electric-type such as Ampharos with Thunder Wave. Paralysis remains throughout the battle while sleep can wear off, but the trade off is sleep makes it easier to capture the Pokemon. False Swipe always leaves the opponent with at least one hit point, so you won't have to worry about accidentally knocking out the legendary Pokemon. Disable lets you rid the legendary Pokemon of one of its irritating attacks. In addition to these two Pokemon, bring along Pokemon with a superior type-advantage over the legendary Pokemon in question.
Always keep a large supply (at least 30) of Ultra Balls, as well as Dusk Balls for night hunts and Heavy Balls for larger Pokemon.
Most importantly: always save your game right before initiating combat with a legendary Pokemon. You can always reset and try again if you fail.
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Ho-Oh and Lugia
After getting the Rising Badge, you'll get a phone call on your Poke Gear instructing you to head to Ecruteak City. Fly on over to find the Kimono girls waiting in the dance school. You may remember running into these random Kimono girls throughout the story. As they'll soon reveal, they've been surreptitiously spying on you to determine whether or not you're worthy of capturing a legendary Pokemon--but first you'll have to battle them. They each have one level 38 Eeveelution (Flareon, Jolteon, Vaporeon, Espeon and Umbreon) and you'll have to battle them all consecutively without a break. Take them out to earn either the Clear Bell (Pokemon Heart Gold) or the Tidal Bell (Pokemon Soul Silver).
In Pokemon Heart Gold, go to the Bell Tower in the north of Ecruteak City. Climb all the way to the top, picking up a handful of useful items along the way if you wish. When you reach the roof, a pretty little cut scene will ensue and Ho-Oh will arrive. Save your game and step forward to initiate battle with the level 45 legendary Pokemon. Ho-Oh will succumb to water, electric or rock attacks.
In Pokemon Soul Silver, go to the Whirl Islands, found by surfing east from Cianwood City. You'll need the whirlpool and surf abilities to make it through to the main chamber. Again, a short cut scene will ensue and a level 45 Lugia will appear. Save your game and then challenge it. Lugia will be weak against rock, electric and ice attacks.
You will later have the chance to catch the opposite Pokemon (Lugia in Pokemon Heart Gold, Ho-Oh in Pokemon Soul Silver) by getting the silver or rainbow wing in Pewter City. Ho-Oh or Lugia will now be at level 70.
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Legendary Beasts - Suicune
You'll release the three legendary beasts (Suicune, Entei, and Raikou) right before challenging the fourth gym leader in Ecruteak City, but you won't be able to catch them until much later. You will randomly encounter Suicune throughout the story of Pokemon Heart Gold and Soul Silver, but you won't get the chance to capture this legendary Pokemon until you've defeated the Elite Four, restored power in Kanto and defeated the Gym Leader Misty. Head north from the Cerulean Gym to cross the Nugget Bridge. You'll have to battle a handful of trainers as you pass through a hedge maze. At the end you'll find Suicune sitting upon a cliff. Save your game and challenge the level 40 Suicune. Use grass and electric attacks to weaken it.
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Legendary Beasts - Entei and Raikou
Finding Entei and Raikou in Pokemon Heart Gold and Soul Silver can be trickier. You'll encounter them randomly in any area of tall grass throughout Johto and Kanto. Keep a Pokemon higher than level 40 in the front of your party and apply Max Repel. Walk through any area of tall grass until you encounter Raikou or Suicune. Unlike other legendary Pokemon, these two won't stand and fight. If given the chance, they'll use their first attack to flee. You need to use a Pokemon with a high speed stat to induce sleep with Sleep Powder or Hypnosis before they can get away. Weaken Raikou with rock or ground attacks and weaken Entei with water or rock attacks.
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Legendary Birds - Articuno, Zapdos, and Moltres
Capture Articuno, Zapdos and Moltres after collecting all 16 badges found in Pokemon Heart Gold and Soul Silver. All three will be at level 50. Articuno dwells in the Seafoam Islands to the east of Cinnabar Island, Zapdos sits right outside the Power Plant, and Moltres can be found within Mt. Silver to the west of the Pokemon League. Weaken Articuno with electric attacks, Zapdos with rock attacks, and Moltres with water or electric attacks.
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Mewtwo is the most powerful legendary Pokemon available in Pokemon Heart Gold and Soul Silver, and you'll be able to take him on after collecting all 16 badges. You'll find him in the Cerulean Cave, accessed by surfing from the north of Cerulean City downstream to the cave entrance. Mewtwo appears at level 70 in Pokemon Heart Gold and Soul Silver, and can be incredibly difficult to capture. Consider using the Master Ball from Professor Elm. You won't find a better instance to use it.
This guide helps you capture all Pokemon in Pokemon Heart Gold and Soul Silver. Part 1 will cover all legendary Pokemon native to Johto and Kanto while part 2 will deal with all legendary Pokemon from Hoenn and Sinnoh.